Warped Mirror
by Lone-ranger1
Summary: When John Sheppard and Rodney McKay are drawn into a dark alternate reality, they've got to blend in to survive. There's more than it seems though and they may never find their way back home. A reality they never could have envisioned will show them just how lucky they really are... and what they could be missing. Shep&McKay Whump. Rework of previous fix COMPLETE.
1. Disbelief

**Warped Mirror**

_**Summary: **__When John Sheppard and Rodney McKay are drawn into a dark alternate reality, they've got to blend in to survive. There's more than it seems though and they may never find their way back home. Shep and McKay whump._

_**WARNING:**__ This story contains mention of non-con, torture, graphic violence, and some minor and recurring character deaths, The story line becomes rather dark so be prepared._

_**Author's Note:**__ This is an edited version of a fic I wrote a long time ago. I've always held a special place in my heart for this story and as such, decided to give it a tune up. If you haven't read this before, enjoy!  
_

* * *

**Prologue**

"Ronon, Teyla, you guys through yet?" John kept the Jumper at a low altitude. If Ronon and Teyla weren't through the gate yet, then he'd swoop in to pick them up. Teyla's smooth voice came in. _"Yes John, We have returned to Atlantis and are awaiting your Jumper and supplies."_

_"Come on Sheppard! I want my wine!"_ Ronon cut in on the radio, not caring who was listening in.

Rodney, who was seated next to Sheppard, rolled his eyes and spoke. "Oh, so I guess the Naquadah we're bringing back is nowhere near as important?"

_"Nope."_

"Settle down you two." John chuckled as he eased the Jumper forward, no need to go top speed. The radio was supposed to be for more official purposes but it's not like this was crunch time. "I got your wine Chewy and just so you know I'm taxing you half of it."

_"I do believe I should try and be with my people tonight."_Teyla muttered over the radio. "_I foresee many headaches tomorrow."_

The group had finished trade agreements with the people of this planet, colloquially named New Caprica as just like it's namesake in the reimagining of Battlestar Galactica, it was nestled within a nebula. The people were relatively friendly, but hesitant to trade with Atlantis. John had personally gone to negotiate, and after many tense hours of deliberation that nearly exhausted his reserves of patience, an agreement was reached. The Jumper's hold carried 400 pounds of refined Naquadah, as well as another 300 pounds of a random assortment of foods and drinks. They'd be back with medicines as well as an engineering team to improve the village's construction techniques and mining efforts.

"Lucky you Teyla, I'll tell you all about it when you get back." Rodney shot an annoyed glare at John. "Hopefully it'll be better than last time we partied on New Athos."

John rolled his eyes, and pushed the jumper away from the settlement. "Oh please, you _cannot_ count that time. How was I supposed to know you had to dilute the stuff before you drank it?"

Ronon scoffed as he laughed over the radio. _"Maybe when you started taking your pants off in front of Carter after the first glass?"_

Laughter erupted over the radio; John cursed the eavesdroppers and decided to change the subject. "Err, yeah well, it was hot. And it's not like I didn't have shorts on underneath. 'sides; didn't you end up getting your hair done by Jinto and his girlfriend?"

Now even more laughter, John could imagine the look on Ronon's face and the beating he'd have to endure later in the sparring room. _"Uhh, let's not bring that up."_

"_Gentlemen…" _Finally, Woolsey's voice overrode any other laughter or banter on the channel. _"…you can discuss each other's hair and trouser condition in private, please use the radios for official communications only."_

John again rolled his eyes and kept quiet. While he did respect Woolsey to a point, the man's insistence on constant official protocol was a headache waiting to happen. During crunch time he knew his men were more than capable, but fun kept them in high spirits. He looked ahead to the landmass where the gate was and saw a bolt of lightning cross the clouds. "Rodney, that storm wasn't there an hour ago."

"What am I, The weather girl?"

"Thank heavens, no."

Rodney grumbled and pointed out the window. "It's a storm, nothing new."

"Is it dangerous?"

Finally Rodney began to work on the console ahead of him. John rolled his eyes, but paid closer attention. "Lets see, it's a pulse storm that's being created by the solar winds pulling the air in an updra…"

"Nyah!" John shirked his shoulders and turned to Rodney. "I didn't ask for its life story - Is it dangerous?"

Rodney made a similar irritated face back at John. "No no no, well… maybe, just keep us low and there shouldn't be a problem. Although…" He continued checking on the console, bringing up readings from the Jumper's sensors.

John kept the jumper at the low altitude with the trees towering nearby; he didn't like how Rodney ended his sentence. "Rodney?"

Rodney ignored him, and continued his scans. When he saw the electromagnetic field around the gate he murmured. "Fascinating…"

"Facinating?" John said. "What are you, Spock? Is it dangerous or not?"

"Figures you'd be Kirk." Rodney shook his head, but then clenched his Jaw. "And no, I don't think it's dangerous."

John didn't like that either. "You don't _think_? Rodney, we're carrying 400 pounds of potential high explosive – I need you to be sure." He began to consider backing off. Ronon could wait for his wine.

"Go! Don't worry about it! The jumper is shielded from electrical disturbances. How else does it fly in space?"

John clenched his jaw, and set the auto-pilot for gate travel. "Alright, if you're absolutely sure…"

"When have I ever…?"

John turned slowly and gave him the best _'you don't want to finish that sentence'_ look. Rodney silenced and looked ahead.

The jumper moved ahead slowly, and John kept his mental interface focused on the sensors. The slightest warning and he'd…

***WARNING, MAGNETIC DISTURBANCE DETECTED***

John reeled from the shock, the Jumper's computer was screaming it at him and even though he tried to move the Jumper away, the controls weren't responding. "Rodney! I've lost control! Something about a…"

"I know I know! I heard!" Rodney began to freak out as well. " Give me a minute!" His fingers flew across the console, trying to work some kind of workaround.

"We don't have a minute!" John looked ahead; the lightning was being attracted by the open gate, and bolt after bolt slammed into it giving off some kind of weird lensing effect. John kept trying to get the jumper to move off, but the pods had already retracted and the jumper was going through the gate. "We're going in!"

John braced himself for anything, and before he knew what exactly had happened, he felt the distinct feeling of going through the gate. Something was strange though, almost as if his entire body was flash fried and rebuilt differently. He didn't have a chance to think about it though, as he quickly lost consciousness.

* * *

"Sheppard! Lad, are you alright?"

John groaned, everything hurt, but that was a good sign, no spinal damage. The distinct smell of burning metal, smoke, and taste of blood in his mouth was enough to judge that the jumper had crashed. He didn't dare open his eyes yet; he always kept them closed until he felt everything else was ok. John could feel the pain fading already and muttered instinctively. "Ugh, I think I got whiplash."

A pair of hands came down on his neck, squeezing various parts and generally assessing him. "No, I don't think so."

"In my _ass!"_ John answered bitterly with the reference, batting away the hands only afterwards realizing who he was talking to. "Wait, _Carson?"_

He opened his eyes and looked at a confused looking Carson Beckett, who with another 2 medics was pulling him out of the crashed Jumper. Everything had a strange darker hue, but it wasn't his eyes, the walls, ceiling, and even Carson's uniform were darker. He couldn't focus on his surroundings, only on Carson and his injuries. "Aye, your ass is looking pretty banged up, but you'll be fine in a wee bit."

John was feeling better, a lot better. Did Carson already give him a painkiller? "Wha… how… the hell are you doing here? I thought you were back on Earth." Before Carson could respond, John remembered Rodney. "McKay? Damn it, is Rodney alright?"

Carson nodded, but his face showed something strange, almost hostility. "Aye,_Doctor McKay_ will be alright lad. Not more than a few bruises and bumps. He's got a horseshoe up his arse that one."

If John didn't know better, he would have sworn Carson spit at McKay's name. "The hell happened?"

The medics placed him on a stretcher, and a sudden bright light blinded him momentarily. John was still unsure of where the hell he was and his whole sense of direction and position was discombobulated. Carson's voice carried as he was moved. "Ain't it obvious? You crashed lad! Right through the gate and onto the stairs! Hell, you nearly flattened Chuck if he hadn't jumped out the way. I'd be peeling him up with a spatula otherwise." He finished on a humorous tone.

_That_got John's attention. Carson was a Doctor first, and a dark comedian last. He'd never make a joke about someone dying. John wanted to say something, but now as he was getting his senses back to normal, he realized that he wasn't in his home.

The gateroom looked very different – dark banners flowed along like decorations, and marines manned machine gun emplacements as well as other strange looking weapons. They wore dark body armor with cables wrapped around them. John had never seen anything like it. They all looked at him with concern, but with an air of respe…

_No…_ it was _fear_. For some reason they feared him. He could see it in their eyes. It was the same look Doolie Airmen gave Colonels and Generals.

The pain was almost gone; in fact John felt he could probably run again. Something was very wrong. He blinked away the pain from his eyes and looked around more. His suspicions were confirmed when Lorne walked up to him and saluted. "General sir, we received McKay's report on the depth of the Naquadah strain on the planet. Daedalus is standing by and Larrin is waiting for your order to deploy."

John did a double take. "Say again?"

Lorne got a worried look on his face, and he pulled Carson over from another stretcher. "What happened to General Sheppard? He's acting funny."

Carson looked at John, and shrugged. "I'm not sure, Colonel… until I get him under a scanner I can't tell for sure. Perhaps some memory loss."

John became indignant. "_I'm_ acting funny? Since when am I a General and you a Colonel? And _Larrin_, on _Daedalus_?"

Lorne raised his eyebrows in shock, and muttered softly, but John was still able to hear. "We do not need this right now Doc. _Fix him._ I don't care what you have to do just get it done." He turned away and hit his earpiece. "Commander Larrin, You have a go for orbital bombardment. Commence resource extraction."

John tried to get up, but a pair of sentries who seemed to come from nowhere held him down as he yelled _"What?_ Orbital Bombardment? The _hell_ is going on?"

"Get a hold of yourself lad, you're just confused." Carson got closer, and the smile on his face made John suddenly fear what was happening. "Here." Carson flicked out a large syringe. "This'll calm ya down."

Despite fighting back, John felt the small injection into his thigh, almost instantly he felt the sedative begin to take effect, quickly losing all feeling in his legs. Before he could really argue anymore, the lights faded, and he drifted into a dreary sleep.

**-Chapter 1 - Disbelief-**

_"__Sheppard! Sheppard wake up! Damnit wake up soldier!"_

John groaned again, the trailing effects of the sedative Carson had given him was wearing off quickly, but he still felt the dryness in his mouth, and the crusty material on his eyelids. "Rodney?"

Now he felt the trembling, Rodney's hands were shaking him awake, almost desperately. "Yes! Come on, shake it off!"

John did not like getting woken up like this. His brother David had once woken him like this after a night of drinking and John had thrown a full force punch. Dave's nose never did completely straighten after that. "Stop, stop it! Dammit McKay let go of me!"

He opened his eyes, and rubbed away the hard material that had caked onto his eyelashes. He was in the infirmary on a bed, but still in his BDUs thankfully. He felt stubble on his face and wondered how long he'd been out. John looked to McKay and instantly recoiled at how different _he_ looked. _"__Jesus Rodney,_ the hell happened to you?"

Rodney was standing in front of him, with a massive scar running along his face from the left of his chin to his right eyebrow. Most of his hair was missing, and his complexion was terrible. He was a lot skinnier as well, almost emaciated. "I'm trying to tell you! Dammit Sheppard this isn't our Atlantis!"

John rubbed his face and recoiled away in surprise. Instead of his stubbled face he expected, he felt a distinct trimmed beard and mustache coating his chin. He shook it off and looked around – the whole infirmary looked strange, almost overstocked and _busy. _Equipment he'd never seen before beeped and whined, but he needed to focus. Rodney grabbed hold of his wrist and forced him to look him in the eyes. Rodney's eyes… they were almost whited over. "Holy crap… where the hell are we?"

John looked around as he listened to Rodney. "I don't know, but these aren't our bodies either, you've got a beard and some kind of healing ability, and I'm… well I'm five minutes from a bad zombie movie!" Now looking around and examining the differences, he could see this infirmary was _very_ different. There were more ancient devices around, and other technology John had never seen before. "This is crazy Sheppard. I don't know the full story, but Atlantis is in space!"

John sat up straight, and felt a strange tingling in his body. "In space?"

Before John could further question him, Rodney shushed him as Carson was approaching having heard the commotion. "Aye, good to see you lads up and about. Should have left a guard or two to keep an eye on you. I know you hate me house'o'horrors." Carson chuckled at John, but frowned at Rodney.

Rodney spoke before John, his voice a bit hoarse and forced. "Yes well… the General and I should be fine thanks to your quick work."

Carson scoffed, and rolled his eyes. "Oh don't bother kissin' me ass McKay; I've given you all the painkillers you can handle. Another month on the outside, and we'll be free of your pestering."

John couldn't even begin to comprehend. If the situation were any different, he would have thrown a punch in anger. "Another _Month_?"

Carson looked and John and sighed. "Aye lad, seems you've had a bit of memory loss. Our scans show no brain damage or any other injuries so I suggest you go back to your quarters and let the wee guys do their work in peace for a day or two, Colonel Lorne has offered to handle things for now until you're back in ship-shape." He looked to Rodney. "As for you, I'm sure there's something in your lab you can waste the last bit of your life decoding. You're cleared for duty." He turned around and walked away, John fumbling over his both kind, and harsh bedside manner.

John got up off the bed, wondering where all the nurses and his friends were waiting for him. Instead it looked like only a few marines were nearby, watching but not doing much else. Since when did the infirmary need guards? Since when had Carson ever let him _walk _out of here without a million tests and nurse and orderly support?

McKay limped over around the bed, John now realizing he had a cane. "I don't have any idea what's going on Sheppard, but I think we should play it smooth for now until we know more, everybody seems to hate me here."

John patted himself down, what had Carson meant by 'wee guys'? "Yeah… yeah I umm… Damn McKay, how do we get outta this one?"

Rodney shrugged, and winced in pain. "At least you're in decent shape. From what I can tell I'm in the last stages of radiation poisoning. He wasn't kidding about painkillers. I'm hopped up to my eyes on oxycodone." He had a defeated look in his eyes, John didn't blame him.

Taking him by the arm, John led McKay out, unsure of whether or not to help the suddenly frail looking scientist. More than a few people gave them strange looks, as if it was shocking that he'd help the injured man.

Once they were out in the hallway and alone, McKay began to explain. "It must have been that magnetic storm. Somehow we switched bodies with our counter-parts in this reality. Lorne said you went because you wanted to show that village why they should join us, but they didn't want to get involved. Guess it didn't work because Daedalus bombed what little defensive capabilities they had from orbit and just took what they wanted." He shook his head and looked shocked. "Apparently you took me because everyone else was busy with more important things. I don't even think I have a rank in the civilians…"

John again felt the beard on his chin, and noticed a small bald spot along the edge of his lip, almost definitely a scar. "God_damnit_… I'm Evil Spock aren't I?" He looked to McKay in horror.

Rodney on the other hand scoffed. "And I'm Trip from Enterprise! All I'm missing is a hot Vulcan sex slave!"

As if summoned, Katie Brown suddenly appeared at the end of the Hallway. "Rodney! Oh my god Rodney! Are you alright?"

John cocked his head to Rodney and clenched his jaw. "Careful what you wish for McKay…"

She ran up to them, and quickly took Rodney from John's arm. She seemed so worried over him, and quickly took care of helping him along. "I heard what happened! It's so lucky you didn't get hurt in the crash!"

Rodney scoffed, but gladly accepted the help. "Yes well, Carson says I've got 'a horseshoe up my arse', and I'm beginning to think that's a good thing!" John couldn't help but snicker, though he still felt bad.

Katie wrapped her arm around him and tugged him along. "Come on Rodney, you should get some rest."

Rodney fought her off for a moment, and stared her straight in the face. "Just give me a second alone with Col… I mean… _General_ Sheppard…"

John was nowhere near used to it. It had taken awhile to get used to "Colonel" Sheppard, _General_ was a complete mystery to him. The look of fear in Katie's eyes at his words made John feel the need to reassure her "Yes… I promise I'll go easy on him."

Katie looked to John; again, the fear was there. For some reason John was feared on this base. He didn't like it. "Umm… Okay… please General…" She moved off, and quickly left earshot.

Rodney grabbed John by the sleeve and pulled him closer. "Listen, this place doesn't feel right. I'm sure you've noticed the huge amount of guards all over the freaking place. It's been almost 3 hours since Carson knocked you out and from what I've seen, we don't want to expose ourselves. They even had a team ready for cleanup of the crash, as if it's a normal thing!"

John shook his head, still confused. "Well if we tell them we're not the people they know, maybe they'll help us get back!"

Rodney's eyes said the whole story. "I was going to try that… but I don't think it'll go over well… Look at them Sheppard! Look at Carson; _he hates me!_ I mean he'd probably kill me if he had the chance." Rodney looked intensely depressed; this reality had really kicked him in the stones. "I really think the only thing keeping me alive is you, Sheppard. They all respect you; I think they're willing to follow your orders no matter what."

Katie at the end looked down and spoke loudly. "Are you almost done?"

"Katie! I'm not done! Be quiet!" Rodney snarked; which John found offensive, but surprisingly he didn't feel like defending Katie, it struck odd to John that he would be so agreeable with this behavior. Rodney seemed to notice it too, and they gave each other a double take after a moment's pause. "Did I just say that?"

John nodded his head in confusion. "Yeah… the hell is happening? I should have smacked you for saying that… and where the hell _is_ everyone? Where's Keller? And Woolsey? Ronon and Teyla?"

There was definitely something weird going on with his thinking, let alone his body and they just simply didn't have the answers. Rodney shook his head, unsure of any of those people. "I haven't seen any of them! It's just us; we're completely alone out here from what I can tell… Look, if this reality is anything like ours, there'll be information in the database about our history. Logs, people, planets we've been to – I can't access anything but my own research it seems, but you're in charge so you should have total access! You need to check it out Sheppard, and once we know more we can do something."

John scratched his head, god this was confusing. Rodney seemed surprisingly focused and even calm despite his circumstances. John was feeling strange, in a sort of nonchalant but fully aware mode. He knew he needed to get back, and that Rodney was going to get them back. But something was telling him no, that this was the place he was needed, and he had to finish a job here before he could go home. "Yeah… Rodney, what are the chances of us getting home? Be real."

Rodney sighed dejectedly. "Oh the usual, slim to nil. Once I start up my genius brain and get a look at the Jumper's readings I should be able to figure out exactly what happened and how to recreate it. I'm never wrong, remember?"

John scoffed, but again, it felt almost right for Rodney to be such an arrogant ass. "I think we should split up… Carson said I should get some rest, maybe I'll find something in my logs to help us."

Rodney nodded, and waved Katie over. She gingerly jogged closer, happy to take Rodney off John's hands. "Katie! We're done! Let's go!"

John watched as Katie took the abusive words from McKay with apprehension, as if scared to say anything just yet. SHe helped the now feeble scientist off. John stood there for a few moments before deciding to try and get some information. He grabbed his earpiece and tapped a com line open. "Ma… _Colonel_ Lorne please come in." John winced, he would have to get used to this new higher ranked Evan Lorne.

_"__General? Is that you?"_

"Yes… I think we need to have a little chat."

_"__Yes sir, I'm in Ops Center right now, we can talk privately in your office here."_

"Uhh…" John pinched the bridge of his nose, slightly embarrassed. "Remind me where that is?"

"…_The gate room, sir. The office across the control room?"_

"Oh." John really felt lost now that he looked around. "Okay, I'll be there soon."

"_Yes sir."_

It was all so weird; _Ops Center? His o_ffice? He'd always thought of it as someone else's; never having to be the big boss. It was Elizabeth's office… Sam's office and most recently, Woolsey's impenetrable fortress of boredom. John found himself wondering what decorations his counterpart in this reality put in it.

The journey to the gate room was quick, Atlantis still being the same design. Everyone he passed gave him a salute, some with a respectful apprehension, others with only fear. John tried desperately to convince himself it was the beard.

Once inside the Gate Room, Lorne quickly led him into the office. The gate room was fully staffed and teams were going in and out, much more so than his own Atlantis was used to. The gun emplacements and racks of weapons were the more disturbing part.

Surprisingly, a full door had been installed in the office and the glass windows had been coated over with a matte film. John looked around the office and instantly felt comfortable. On the walls, different pictures made neat rows. Some faces he recognized, others he didn't. All of them were from Pegasus, with only one distinctly being from Earth. He saw pictures of himself with Sam and Larrin hanging off his arms standing on the Balcony to the gate room with Ford and Lorne beside laughing, a picture of him and Sam standing in the back of a Jumper, posing in what seemed a intimate shot as she had her almost sad face on his shoulder, and still a last one with Teyla and most of the Athosian children gathered around John, a football in his hands and a giant smile on his face. These were only a few among more that featured various other worlds he recognized.

Most prevalent though was the one from Earth, it showed someone he hadn't seen in awhile. General O'Neill. But he looked different, instead of his traditional formal military wear; he had something akin to the same heavy body armor the Marines here on Atlantis wore. Even more, the picture showed O'Neill standing on a podium that distinctly said _"Terran President."_ The bullseye drawn around O'Neill's head alarmed John, as did the darts stuck into the image.

Lorne must have noticed him checking out the pictures, as he began to explain. "Sir… I'm not sure how much memory loss you've suffered, but I'm hoping you still remember enough to continue our current mission. We need your leadership if we want to stand any chance against O'Neill."

"Against O'Neill?" John felt the lump in his throat grow.

Lorne sighed, and muttered to himself. "Goddamnit… you don't remember, do you?"

John turned to his XO, and before shaking his head, thought about it. "I… no… I don't remember, but I get the feeling it has something to do with him being President."

Lorne nodded, and clenched his jaw. "Yes sir. Maybe if we started with the last thing you remember?"

John considered it. He could tell him what he knew of his own reality, but by playing up the memory loss; Lorne might be able to fill the gaps. "It's weird Evan. I remember names, I remember places… but I don't remember any events… I think I'm gonna need a crash course on Stargate History."

Lorne made a slightly indecisive move with his head, and then nodded uncomfortably. "Uh… Yes sir, if it'll help…"

John noticed his reticence. "Something wrong?"

Lorne furrowed his brow as he closed the door behind him. "It's just… you haven't called me Evan in a long time… John."

John sighed, and sat down in the chair behind the desk. "I don't doubt it… It's not often I use it."

Lorne stood before the desk, and made a dejected sigh. "It's my fault, sir. We should have just taken what we needed instead of sending you to give them an ultimatum. I thought maybe if you showed up they might see it as a sign of respect and join up, but I guess they just didn't see reason. Larrin's got all the Naquadah she can hold already and she's heading back… I'm ready to receive any disciplinary action you may have for me."

John furrowed his brow, and contemplated what Lorne was saying. _Is he saying I wanted to just blast that village off the face of the planet and take what I wanted? And i'm willing to punish him for not listening to me? The hell kind of man am I here?_

"I should have listened to you, sir." Lorne continued. "This is war and we don't have the luxury of always being able to do things the nice way."

John didn't know what to say. All he could do was listen. "We'll see… just start from the beginning."

The beginning turned out to be almost 15 years earlier, during the original Abydos mission with Colonel Jack O'Neill and Daniel Jackson. It had taken longer in this reality for it to be concluded, as Ra had spent considerably more time torturing the survivors of the team for information. Colonel O'Neill in particular had gotten the brunt of it and nobody really understood how he coped. Finally after several months, the outcome of that mission was a fully loaded Goa'uld Mothership that then Colonel O'Neill managed to steal from Ra, having killed the false god in a long term plan.

The ship was brought back to Earth and studied, with the American government quickly reverse engineering many different aspects. It wasn't long before this attracted the attention of more Goa'uld and the Stargate Program entered full swing. The biggest difference was that the people of the SGC weren't the honorable people John was used to. Lorne told him of his own missions to steal technology while attracting the least amount of attention from the Asgard.

Over time, the Humans began to develop a serious power base in the Milky Way, The American government joined with the Chinese and British empires to lead the world in the Stargate program, giving their full commitment and resources to protecting Earth.

The Stargate program was made public shortly after the capture of Apophis and the subsequent publicly aired execution of said false god by new Jaffa allies. With the world turned upside down, religious extremism and smaller 2nd and 3rd world countries began a civil world war.

The military took over, and pretty soon the SGC became the sole unifying government. Things went on a similar note to John's own reality, as far as alien races and contact was concerned, up until the assassination of most of the command staff of the SGC in what was called a terrorist Jaffa attack. After this, Colonel O'Neill was promoted to the head of the SGC with his experience and connections, and soon after, unanimously voted to be the voice of the people in any off-world dealings.

Nobody knew exactly how it happened, but the Asgard had suddenly disappeared. O'Neill's first action was to sponsor an expedition to the Ida Galaxy and after a year, came back with all their technology and no idea where the Asgard had gone. Over time, it became clear that O'Neill had become a dictator, changed very much from the man John knew in his own reality.

John himself had been discovered through a military wide program to find people with the Ancient Gene. At first they thought he was just like any other, but soon it was evident his innate ability to control the Ancient Technology far surpassed anyone on the planet. His brother David had been checked as well, but only came up with a nominal strength gene. John was unique.

When the Atlantis Expedition was sent out, it soon became clear that this was yet another control that President O'Neill used, getting rid of all those with the Ancient Gene naturally and marooning them in another Galaxy meant that Jack would have sole control of the highest Ancient Tech in the Milky Way - just more evidence of the totalitarian state O"Neill had created beneath him.

Lorne stopped here, after almost an hour and a half of explaining. John couldn't believe it. But he was forced to pretend to in order to keep appearances up. "So… we're completely on our own then?"

Lorne nodded, and yawned. "Daedalus came a year after our arrival during the replicator Siege, and that's when we finally figured it out. You led the revolt and I followed. O'Neill is a madman and he doesn't deserve our respect, or loyalty."

John gulped, _'Replicator siege?' _He remembered his own version at that same time with the Wraith – losing Ford, and again the almost suicidal mission he embarked on. He wanted to ask where those people were… Most of all Elizabeth… maybe in this reality she was still here, or if not here, then back on Earth.

But it was getting late and he was getting tired. He figured his logs might have details on his own missions here in Pegasus as Lorne had given him only the most general of knowledge. "Well, thank you Colonel, I think that jarred some memories loose. If you'll do me the favor and stay in command till I'm back to normal?"

Lorne nodded, and scratched the stubble on his chin. "Yes sir. I'll remain on duty until you feel better, although the sooner you take control back, the sooner we'll be able to move ahead with our plans."

John wanted to know those plans, but he wasn't ready for that. He was still reeling from the shock of learning part of an alternate history, and his beard itched something furious. He dismissed Lorne and left for his quarters.

This place was insanity. Replicator siege? What had happened? Where was Sumner and Caldwell? How had Larrin ended up Commander of Daedalus? Where were the people he knew and loved as his family? Where was Elizabeth?

It was very strange to look out the window and see stars. He was so used to seeing the horizon that it gave him a sense of vertigo. It wasn't long before he ended up in front of his quarters, wondering what insanity lay inside.

He opened the door, and was relatively relieved that everything looked normal. Except for the extra space, and the computer console festooned with complicated looking equipment, they were the same as his old quarters.

He didn't bother with the lights, and took his shirt off. John looked at the strange uniform; it was black like his regular BDU's back in his own reality, but with different markings, and different insignias. The star on his shoulder pads indicated his rank… Brigadier General.

He still couldn't believe it. He still didn't have all the facts. Why had his counterpart decided to revolt and take this place by force? John was tired, but needed to know. He looked to the computer, and sighed as he sat down.

Logging on, everything was the same. His password, the background image of Johnny Cash's first album cover, and even most of the folder names. There were plenty of other new ones he'd never seen. But the one he looked for… Logs and Mission Reports… was still right where he thought it would be.

He opened it, and saw the same reports he'd filed before, except these were video files. That was different. He looked around and found a headset. He also noticed a small fridge built into the desk and opened it. Bottles of what looked like beer, water, as well as a few tupperwared meals were inside. Opening a bottle of what smelled like beer, he sat back and opened the entire folder of his first year here, ready to watch as many as he could.

* * *

**Arrival to Atlantis – Day 1**

_"__Well… this is the first log I'm making here. The lost city of the Ancients… it's everything I could have imagined and more. I've spent all day interacting with the systems and it's amazing, even though it's all in gibberish to me I can sorta understand what each system does just by feeling alone._

_Sumner has made it clear that's the only reason I'm here. He still doesn't trust me. I don't trust him either, something's up and I'm not going to like it when I find out…_

_Evidently we're boned, but that was to be expected since we can't dial back Earth anyways. The Ancients who left this place figured they'd be back and left the damn city underwater! The shield surrounding this place is almost drained, and with our generators backing them up, we've got a week on the outside to find more energy sources._

_Sumner's been busy setting up teams and he's put me on his along with Lieutenant Ford and Sergeant Bates. Ford I can stand, he's just a kid with a steady trigger finger. Bates is an asskissing sonofa… whatever. Not like I have much choice._

_Dr. Weir and Dr. Beckett found a holographic emitter, some old Lady was telling them about the history of this place and how the 'Lanteans' got their asses handed to them by some 'enemy'. I gotta admit, I didn't like hearing that._

_Well I've got to catch some rack time before the mission. Going someplace called 'Athos' tomorrow. Hopefully we'll find some Zero Point Energy Doodads or whatever McKay said they were called. Here's hoping this isn't my last log entry."_

* * *

John silently sighed, it was similar to his own log he'd made years ago, but darker, and with more hatred in his voice. Something told him he wouldn't like where the rest of these went. The next log started, and he paid silent attention.

* * *

**Atlantis Log – Day 3**

_As Bender likes to say, we're boned. Yesterday we found a village of people on Athos, and Sumner and Bates got on their nerves pretty quickly. Thankfully their leader… Teyla… was reasonable and I managed to talk her into not chasing us off._

_She showed me an old cave while our guys explored, and I found an old necklace she'd lost… and that's when all hell broke loose. Teyla could feel as 'They' showed up. The Wraith, the enemy that defeated the Lanteans ten thousand years ago according to Weir. I wasn't there for the initial contact, but they grabbed Sumner and a bunch of others including Teyla with some scooping transporter beam._

_Bates took one of those ships down, say what you will about his social skills, that couldn't have been an easy shot. The other two ships got away through the gate and Ford managed to catch which symbols were lit up. I figured losing my commanding officer on the first mission we were on reflected pretty badly on us, so once we got back to Atlantis, I got a heavy strike team ready._

_The Wraith are something else entirely, Space Vampires? You gotta be shittin me, but there they are. Feeding on the 'life force' of humans. Fuckers are hard to kill, that ship Bates shot down? Goddamned __**severed hand**__ tried to attack me. Talk about an Addams Family moment. Beckett gave us a little biology lesson and it basically amount to this. Shoot them – a lot._

_Weir didn't want us to go, and McKay babbled something about permutations. Negative whiners. Weir came around though, and a little arguing got McKay to see things my way. McKay had also found a way to actually get the city to rise up out of the ocean, so that's one certain death problem solved. The air on this planet is so fresh…_

…_not like that Wraith planet. We went in using a Jumper. And McKay, since I know you're probably going to see this eventually, Yes, I know Gate Ship is more technical and sounds formal, but come on, it's a big puddle, and it jumps from one side to the other. That goes for you too Ford._

_That thing is amazing, the mental interface lets me actually see the air and space around me in a full 360 degrees while being aware of it all. It's like nothing I've ever flown before. Doesn't make me a turkey sandwich though so I'm just a tad bit disappointed. Even the 302's are nothing compared, although they're still faster._

_Once we landed, we moved in quietly. The ship had some scanner we're calling 'Life Signs Detector' for now that I used to track our people down. The Wraith had a big ass lab in the forest, and we got inside pretty fast._

_I'll say this about the Wraith, they're monsters. Teyla was right when she said they're abominations. We lost 2 men in there, and uhh… apparently I woke up a whole lotta Wraith from some hibernation… but we got our people and the Athosians out._

_We almost lost Sumner, Damn Wraith bitch was about to… *sigh*… thankfully I had a good shot – If I'd hesitated it would have been a lot worse. He owes me one but won't say it. Bastard. We got them all out ok and managed to make it back to Atlantis in one piece. Most of Teyla's people came too since Athos is probably high on the Wraith list of places to go._

_Sumner doesn't really trust the Athosians, but me and Weir convinced him to let them stay for now. They helped us, and are willing to keep helping us. We're completely cut off from Earth and it's just us out here. Sumner put me in charge of the Marine Contingent, and also 'Atlantis Recon -1'… guess he does value me a little. I've got Ford, McKay, and Teyla as my backup. He wants us to explore and see if we can find any more technology, especially ZPMs._

_That's it for now really. Weir promised to open that ridiculously oversized champagne bottle so I better go before it's all gone."_

* * *

John remembered that night, and talking to Weir about having to shoot Sumner. In some ways it seemed his counterpart had it easier. He opened the next file.

* * *

**Atlantis Log – Day 6**

_"__It's been busy, haven't had any time to update this. McKay screwed up, again. But at least he pulled it through in the end. I gotta admit, I wasn't expecting him to do anything even remotely like that._

_As far as shooting him with that shield on; I can't, nor shall I even attempt to deny that it wasn't great fun. Grodin had fun trying to punch him too despite the singed knuckles. Sumner still doesn't trust the Athosians, but for the moment it doesn't really matter. Now that that crazy energy mist creature thing is gone, we've got some semblance of peace on this base._

_The Marines are restless, so I set up a little firing range for them. The braver Athosians along with Teyla started their training today, hopefully Sumner and Weir can see that they're more than willing to join us._

_That kid Jinto kills me, half the world's best scientists on this base, and the kid figures out how to use the base transporters 'fore we do. Go figure. I love that little guy. Doesn't like football too much though… gotta remember to not mention hockey again._

_We should be starting our exploration in the next few days. Hopefully we can find more ZPMs and get this place running at full. McKay might be like a kid in a candy store with all the devices all over the place. But I feel something… maybe it's just my imagination, but I feel comfortable here. Almost as if the city itself is welcoming me…_

_Well before I sign my own section 8, I've got to go to sleep. Teyla mentioned something about Banto Stick sparring tomorrow. By far the best time of my day is watching her move so… Yeah… Shower time."_

* * *

John chuckled, and wiped the forming tear on his eye. It had been awhile since he saw Jinto, and he wondered how the young man was doing back in his own reality… or if he was even still alive in this one. The next log started, the time code was a day John would never forget.

* * *

**Atlantis Log – Day 10**

_"__I hate the Wraith. I hate Bugs. And I hate Kavanaugh. Sumner is acting alright and Ford's tougher than I thought. That. Is. all."_

* * *

John smirked. Pretty much exactly what he had back home sans the Sumner. The next few logs were nothing interesting, more complaining about Sumner, 10000 year old plants, and dozens of other small things that weren't any real important information. He noted slowly that his logs got less and less cheerful, and more and more angry. His beard appeared about halfway through.

In fact, except for Sumner being there, just about everything else was the same. The children on the EMP planet, the uselessness of their ZPM, the suspicions put on the Athosians by Bates, the first encounter with the Genii… that is until the log about the events of the Storm and Genii attack.

* * *

**Atlantis Log – Day 163**

_"__The storm is over… and the Genii are gone. We lost 4 men yesterday, and Weir, Teyla, and McKay are all in the Infirmary._

_Sumner gave me a field medal, Silver Star for valor… I wasn't expecting that. He said I saved the expedition, and maybe he was wrong about bringing me along… I'm not so sure._

_I killed more than sixty men yesterday… I might not have seen most them, but I've got to live with that. The Genii hate us now, and Sumner thinks we should consider a pre-emptive retaliatory strike. As much as I hate to say it… I think he's right. We can't afford to fight on two fronts. McKay insists he can build a nuke for us if we can find some plutonium and some uranium. Or if it comes down to it, he can repurpose one of our Naquadah Generators._

_Kolya's gonna pay. I swear it."_

* * *

John stopped for a few moments, he'd been watching for almost 30 minutes straight and was getting sleepy. He wanted to see what led up the siege though and kept watching.

Unbeknownst to him, the door to his quarters opened, and a slender figure entered, seeing he was busy at the computer, she silently changed clothes before heading into the next room.

John was too focused on the next few logs, and how they were so different than what had happened in his own reality.

* * *

**Atlantis Log – Day 220**

_"__Nanites. Machines a millionth of a millimeter big. Didn't affect me in the least, but at least McKay got to prove he could overload a Naquadah Generator if he needed to._

_Sumner shot down 'Lizbeth's opinion pretty fast. She's pissed I agreed with him. It all turned out okay in the end but I'm starting to second guess Sumner… He's more open now but there's… something. He's hiding something… I don't think him being friendly is… friendly._

_McKay says there's more information on the Nanites in the ancient database. All we need's a ZPM to make up for the one that we pulled out last week to power it. The old ZPM's got enough power for one 5 minute dial to Earth, and we're saving it for an emergency. I get the distinct feeling I'd rather not know what the Ancients did with those little nanite bastards."_

* * *

**Atlantis Log – Day 225**

_"__Sumner's lying. I can tell now. Chaya… she showed me. This is all going to end in a goddamn horror show and I can see it coming… Nobody really trusts me right now, I don't think that'll change until this is over. I almost… I almost wish I could stay with her. I know she wanted me to stay… but she knows I'm needed here._

_I was wrong, a few people trust me… McKay… Teyla… Ford… and for some strange reason… 'lizbeth… This is not going to end well."_

* * *

When it came to the log about the ZPM hidden and worshiped by the Brotherhood, John couldn't believe his counterpart's words.

* * *

**Atlantis Log – Day 285**

_"__I killed Kolya today._

_When we took the ZPM a whole melee broke out, he tried to stab me but my vest blocked it… so I stabbed him right in the chest… it was instinct… pure gut reaction. Stab, twist, pull out sideways… I saw the shock in his eyes. His blood spewed all over my uniform._

_Liz thinks I'm a monster, McKay says I only did what I had to, and the city thinks I'm a hero again. Ford didn't say anything… I think I might have scared the kid. Teyla's been quiet too. In fact she's pretty much stopped talking to me for anything other than official reasons._

_Sumner says he's proud, but we can never go back to that planet. We stole their ZPM and now I've got to live with that decision. If this ends up writing history… then let history show that I did what I thought was right._

_The ZPM is nearly full, we've got 1/3rd power to the city… and thanks to the McKay and the ancient Database, we know where we can get more._

_Asuras… I wonder what we could possibly trade to them."_

* * *

John froze. The Asurans. The Replicators. It was three years they were in Atlantis before they found them… This reality found them within a year. He ran his hand through his hair, and sighed heavily. Obviously they'd survived, but this might explain what happened to his friends.

* * *

**Atlantis Log – Day 300**

_"__Liz isn't back yet, and Sumner's getting worried. We contacted Earth and requested reinforcements. President O'Neill promised us as much as he could send on the Daedalus, new battle carrier. Supposed to have plasma weapons or something… sounds powerful but I'll wait till I see it._

_From what I saw on that planet when we first showed up, we won't stand a chance against them if it comes down to it. Sumner wants me to make a plan to get our people back… I think he's trying to kill me since he doesn't want my regular team to go._

_In fact, only people who naturally have the ATA gene are a part of my team… He thinks I don't notice, but Chaya told me to be careful. Here's hoping this isn't my last log entry… again… and if it is. Fuck you Sumner."_

* * *

The logs ended abruptly, and the next one wasn't for another month and a half. John almost hesitantly opened it, fearing what might be on it.

* * *

**Atlantis Log – Day 347**

_"__They're coming. It's inevitable. McKay barely got us outta there alive… We lost Liz, we lost them all. None of them were left by the time we got there._

_I'm different… they changed me. Carson says I'm infected with and I quote 'Galootin' Nanites' and there's nothing he can do about it since they're holding me together._

_Sometimes I wonder if he's a sadist, but he's always kept us alive. McKay explained it better, they were going to make a complete digital copy of our bodies for reference into their own plans… but they weren't all united. A replicator calling itself Niam… he let us go after a month of that hell._

_Sumner's relieved me of duty. Teyla's come around and been a big help. Ford's taken over for me until… well we'll see what happens with these nanites."_

* * *

John looked down at his hands, and instinctively pulled out the small knife attached to his thigh, he used the razor sharp edge to slit his finger open, and moment after, watched as the nanites healed the injury. "Oh my god."

A voice came from behind, it was soft and feminine, and completely unexpected. He turned suddenly and dropped his jaw in shock. The knife fell to the floor with a clatter and slid under the table. The gorgeous blonde was wearing nothing but one of his longer shirts, she stood in front of him and spoke softly as she moved forward to hold his shoulder. "I just got back, I heard you had a little accident. Everything alright babe?"

John finally managed to swallow the lump in his throat. _"Sam?"_

Sam wrapped her arms around him and brought her face close to his, she was wearing her long hair in a barrette that covered his face as she nuzzled him. "Carson said you had some memory loss… I'm glad you remember me."

John couldn't fight the urge to flinch, and the words came out. "Sam… uhh… this might sound really really stupid… but… what are you doing here?"

He meant in Atlantis, and to an even greater degree, half naked in his quarters. The answer was obvious, but he didn't want to face it. Sam got a hurt look on her face as she crossed her arms in front of her in a defensive reflex. "John? What's wrong? Don't you remember?"

John backpedaled, his arms hitting the wall behind him. This was _not_ something he'd been expecting. _'__Sure I mean… Sam's great and all… but Lorne said she was with O'Neill for his whole taking over the world thing… The hell is she doing here… With __**me**__ of all people! ?'_

"Umm… I want to say yes, but I'm scared to say no… So I'm just going to say, I have no clue what's going on, and I'd like you to help explain things to me."

Sam gasped and covered her mouth. "So you don't remember anything?"

John shook his head, and kept a polite smile, he wondered how silly he looked doing such a move with a beard. "Not a thing, but please, tell me." Her eyes watered, and she sat down on the bed. She was on the edge of tears and John had no clue why. His instincts told him to move forward, and carefully he sat down next. "Hey, look I uhh, I'm trying here. It's not like I'm not… I'm not against this Sam. I jus, I just don't know what happened to…"

Sam murmured. "For us to end up like this?"

John nodded. He'd been trying to go native with these people, but this was pushing the limits of what he called normal. "Yeah…"

Sam wiped her eyes, whatever the reason was it must have been something big. John turned her around and hugged her, trying to show he was comfortable with her even if he really wasn't. She reacted positively to that and muttered softly into his shoulder. "No wonder you were looking at your logs, you have no clue what happened." She waited a few seconds, and finally pushed off him. Wiping her eyes and the rest of her face, she quickly regained her composure. "Keep watching your logs… I'll be in the next room."

Sam got up, and despite obviously feeling terrible, moved towards the doorway to the next room. John got up and followed her hesitantly "Sam wait… can't you just…?"

She turned. "No John, I'm sorry I just… _I can't._ just please, please just, just finish watching your logs. I'll wait for you, I'll wait in the next room."

Sam turned, and almost ran into the next room. John fought his instinct to follow her, and instead just tried to comprehend what had just happened. And now for the first time, noticed something against his chest that had been dislodged by Sam's hugging. He pulled out his dog tags, and besides the 2 strips of metal with his military identity… was a silver ring. And now that he looked closer under the light of the computer screen, one of the strips was from her dog tags.

_'__Oh fuck me… McKay is gonna kill my ass."_


	2. Denial

**- Chapter 2 - Denial-**

John realized that he only had one option. Watch the rest of the logs. Sitting down again, his fingers still going over the ring, he opened the next log.

* * *

**Atlantis Log – Day 360**

_"__They're here. The Shield is holding but we're still waiting for Daedalus. Sumner cleared me for duty so I could man the guns, but there're only a few drones left._

_I've got to try, this is too important to be lost now."_

* * *

The log ended abruptly, not surprisingly as they were under attack. The next log was almost a week later, and a lot bigger than most of the others. The image of the John making it was haggard, as if he'd been up for days.

* * *

**Atlantis Log – Day 366**

_"__It's been a year since I've been here, and so much has happened I don't know where to start. I guess I should start by saying this is the last log I'm going to make under the official chain of command. As of the end of this log, I am no longer a member of the United States Air Force. I accepted the rank of Lieutenant Colonel yesterday and am renouncing it today. I cannot in good conscience… or even alive continue with what I now know.._

_Daedalus arrived 3 days ago after some reinforcements through the gate 5 days ago, we've been fighting off assault after assault just barely. I've gotten no sleep since i'm manning the control chair. We even had to move Atlantis off the planet to get away from the Replicators. Daedalus docked, and their crew joined us in repairing and arming the city._

_This is it, the moment Chaya told me I was here for, Sumner refused to move Atlantis back to Earth despite us being badly outnumbered. Even with the ZPM and Daedalus we don't stand a chance against all these Auroras they pulled out of their mechanical asses._

_So I broke into his office, and I found it. I found the reason he won't take us back to Earth. It was hard to believe, but a few hours ago Lorne came to me and told me the same…_

_O'Neill's insane. He sent us here to die. He __**knew**__ about the Wraith! Daedalus is here just to take the ZPMs, and any tech we've recovered so far. Then it'll just abandon us here to die. He doesn't want anyone who has the Ancient Gene naturally on Earth, he doesn't even care that there's a fucking gene therapy, he just doesn't want anyone to pass it on to their children!_

_Lorne figured it out when Caldwell ordered him transferred to Atlantis crew, he sweet talked their engineer Novak into giving him full access and found out. He's a natural gene carrier too and was going to get left behind as well. He came to me since I technically outranked him and told me the whole story._

_He says that there's a rebellion building in the Milky Way, I'd never have believed it but Cam's gone AWOL and he's the presumed leader of the resistance, O'Neill's a dictator but no one on Earth can fight him since he's got the Ancient Control chair and Antarctica… He's got 4 ships in orbit at all times according to Lorne, no one can even take a pleasure flight without him knowing._

_I don't have a choice anymore. Lorne's sworn himself to be loyal to me, and I believe him. The few people I've talked to are with us as well… they better be since they're natural gene carriers too._

_We're gonna take Atlantis, Daedalus… and we'll see where we go from there._

_I've said it before but I mean it this time. If this is my last log. Fuck You Sumner, and a big and definite Fuck You O'Neill, if I ever come face to face with you I'm going to tear out your heart with my bare hands._

* * *

John wasn't too surprised. From what this reality's Lorne had told him, John was pretty pissed off when he found out about the genocidal undertone of the Atlantis Expedition. Lorne hadn't been clear on exactly what happened that day, but the next log was a few days later, and looked equally large.

* * *

**New Atlantis Log – Day 1, Day 369 in Pegasus**

_"__We did it. I rallied everybody I could… even people who didn't have the gene wouldn't agree with them… We did it. In fact, just about everyone at and below Major joined us apart from the reinforcements from Earth._

_Lorne led half our men and took Daedalus, he had Novak insert a virus to keep the ship crippled and show everybody what was about to happen. The same with Atlantis. Once everybody knew what the real plan was, people made their decisions._

_We started the day with a total of 259 people on the Daedalus and Atlantis put together… there are a little less than 200 now. I don't regret doing what I've done, and I know there was no other way… and the only thing I do regret is that some of those dead had families, people who I've worked with for more than a year…_

_Sumner's dead… I went after him myself. He was waiting for me in his office… with a P-90E. He put two plasma bolts into me before filling my chest with lead. I should have died. I should had fallen to the ground and just left this place. Damn nanites kept me alive, but I felt every bit of pain… not something I'd like to experience again._

_So instead I got back up, ripped the gun out of his hands, and dragged him to the Balcony. He begged me not to kill him. He begged me to let him go through the gate back to Earth and he'd never bother us again. He said he could serve as a one way messenger, to tell O'Neill about what happened._

_I told him he didn't have to, because I was going to tell O'Neill myself… I threw him off that balcony, and he fell down and through the shield. No one saw me do it, but they all know I did. The only evidence is no one found his body._

_Most of Atlantis command staff mutinied with us. I'm giving Lorne command of Daedalus for now, McKay found us a nice planet to land on so we can stop draining the ZPM with our shield. And we still have the list of gate addresses Elizabeth sent us from the past. With any luck we'll be able to hold our own for a good while._

_Teyla doesn't know what to do. We can't dial in the planet Lantea anymore and we have no idea what happened to her people. She's pledged to help us as long as we take her people in… I'm going to do it. We need the crew._

_Ford was with us too, but I think he's shell shocked. He got into a heavy fire fight with a pair of Marines from Daedalus and took a bullet to the leg and stomach. Carson says he'll pull through, but he still killed those two men at point blank range in anger._

_I don't trust Bates too much, but I don't know what to do with him… it's not like he willingly knew about what was going to happen._

_Carson didn't fight, but I can respect that. He might be a dark mother sometimes but he's honest. I'm glad he's decided to stay._

_The others don't really have a choice… it's not like Earth will accept them if O'Neill's in charge… They're trapped just like we are. And they better learn to like it, because once we touch down, and get things settled with the Athosians… O'Neill's gonna get a little taste of his own medicine._

_The Replicators have mostly stopped from what we know. Since we're their only target at the moment, they've retreated back to Asuras for the most part. A few Auroras are still looking, but finding one planet in a galaxy isn't exactly the easiest thing to do so we're safe for now. We're taking this break to regroup… god knows we need a little time to cope with this shit."_

John wondered what his counterpart had meant, and also what he would do in the same situation. When Lorne told him about the orbital bombardment, he felt revolted. But if these are the things his counterpart had been forced to do to survive… No… not even all this would make him… John stopped thinking about it. He had to focus on the shattered woman in the next room. He had a feeling the next log would explain how she ended up here

* * *

**New Atlantis Log – Day 8 – Day 374 in Pegasus**

_"__Brigadier General John Sheppard…. At 38 no less. … If only it were official. After discussing it with Lorne, and the few majors left over from the mutiny…as well as the one colonel we rescued a few days ago… They've decided I'm the one they want to follow. Especially after our mission to Earth. _

_She should take charge... but she's in no condition to do that now. Can't blame her. At least she gave me an answer for O'Neill - the Sarcophagus. I can't tell anyone, it's too easy to excuse what he's done, but she explained what it does to a person's mind. __O'Neill's not human anymore, he's a monster. I understand that now. Just another secret to take to the grave... if these nannies will ever let me get that far.__  
_

_I miss Liz… the way she would argue with me and somehow make me feel better doing it. We never did find out exactly what happened to her. I'm hoping she's still out there… that somehow she got out like us. *sigh*…_

_There's so much to talk about… the last two days have been… unending._

_Since I don't really report to anyone anymore, I'm going to be making this log more personal… if it wasn't so already._

_Two days ago we raided the SGC. Using Sumner's IDC and a fake voice to get them to open the Iris… Me, Bates, Lorne, McKay and a heavy assault team of Marines went through. We moved in hard and fast and took the control room quickly. They all fought us… they all knew we weren't supposed to be there. I only recognized a few people, most of them new and loyal to O'Neill…_

_Maybe a year ago I wouldn't have thought twice. But after fighting the Wraith, the Replicators, and even the Genii… it's so hard to squeeze the trigger when it's an Earth born person. They didn't hesitate to try and kill us, so I'm not sorry._

_The plan was to steal as many Naquadah generators and rare tech as we could, though specifically a new ZPM they found. With the control room, we disabled the self-destruct and locked down the base. I was hoping to catch O'Neill on a trip there, but the arrogant bastard was off-world on his flagship, Enterprise… pretty unoriginal name if you ask me._

_We moved room by room, unlocking the base as we went. More of our men came in as we cleared the base, taking everything that wasn't nailed down. We aren't going to be heading back anytime soon, so everything counted, some of the more esoteric stuff were DVDs, books, chocolate… Hell I even snagged a box set of the whole Futurama Series plus movies and tossed it into one of the bags we were taking. It wasn't long before reinforcements from above started fighting us back. I still didn't know O'Neill wasn't there so I went ahead... nanites kept me going even as I took fire… I wanted to kill the bastard right then and there…_

_That's when I found her… I kicked in the door to his room and had the grenade in my hand, ready to pull the pin and throw. She was in the bed… the bastard actually…he… there weren't even any clothes in the place…! All she was wearing was a little… oh god…_

* * *

John understood. His counterpart had found Sam on the base… in O'Neill's private quarters. The possibility of that happening in _any_ reality made him want to vomit. He watched on the screen as his counterpart, the John Sheppard of this reality fought to keep control, finally showing signs of the emotional abuse he'd taken over the past year, moisture building in his eyes, his veins pulsing with barely controlled rage.

* * *

_"… __She saw me and didn't even scream, her eyes looked like I was some messiah come to save her. She begged me to take her, or at the very least kill her… I… I couldn't leave her there. Not with that inhuman monster. I had to give her my vest just so she… *gulp* *sigh*… the others were surprised to see her, but they didn't question it. They all knew what O'Neill saw in her, and probably guessed as much… she grabbed my pistol right off my leg and fought right by us. She killed 4 people that day._

_McKay finally got what he was after, the new ZPM Earth had found buried in Egypt. From what we can tell and what Carter's told us, they were going to dial Atlantis and send a nuke through… guess we one-upped em there.. We switched out our old one with a minimal charge for that and dialed Atlantis. Carter even helped McKay set a Naquadah Generator to overload. As well as inputted her access code to reactivate the base's self-destruct._

_We lost Bates, he stayed behind to hold off their main response force with his M249. I… I misjudged him. I'm praying I don't make the same mistake again. Since I'm a general now, I've given him a posthumous commendation, and dedicated the Armory to him… I think he would have appreciated that._

_Even if they managed to stop one of the explosions, the other would level the place. We left with minutes to spare and we don't know for a fact what happened. But they haven't tried to dial into our gate, and we're not going to waste power by dialing them, so I'm assuming they still need to dig it out of the rubble – if it's even still intact._

_Carter's in bad shape. Carson gave her a physical as well as a psychological exam and… *sigh* well…she's… it'll take awhile for the scars to heal. She's staying with me for now apparently… she won't stay anywhere else and doesn't trust anyone but me and Lorne for some reason. I'm more confused about me than Evan as they knew each other beforehand. He says he's never seen her like this and doesn't have anymore answers than I do. I offered her a room and a personal guard but… she insists on staying here with me._

_McKay might be a problem since I know they have history, but hopefully he doesn't do anything rash since she's…. She's not normal right now, and if he tried anything I don't think she'd blink to kill him._

_During the day, Sam's been helpful, she gave us a hand installing our new generators, and even streamlining some of our power systems. We've begun to arm Atlantis with just about anything we can, rail guns, plasma turrets, even some jerry rigged missile turrets the Daedalus was carrying. It's sort of a crime to turn such a beautiful city into a warship, but without drones, and no energy to power the other weapon systems, it's all we can do in case the Wraith find us let alone the Replicators._

_In a way, the fact that she's here gives us an even bigger chance against any one of our enemies. She's had the most experience out of any of us and in many ways she should take command. Given the situation though, even she insisted I take over instead. _

_She… she cries a lot when she thinks no one's looking. I've caught her a few times already and she begs me not to tell anyone. I… I can't really do anything but sit with her and… I try and help but I don't have a damn clue what to do… how the hell do you get through to a… shit. To top it off I've been so busy lately she's taken to helping me get used to being in command… won't leave my side if it can be helped._

_She's sleeping now… finally. She's been having nightmares and wakes me up in the middle of the night… I'd be wiped the next day but these nanites in my system are keeping me going no matter what, even though I look like the 7th circle of hell as Carson likes to put it._

_In more official news, Daedalus finally made it to Lantea… they had to drop their own gate to the mainland to report in. Only about half of the Athosians survived. They hid in caves to avoid the Replicators, Daedalus is bringing them all back so they can be safe here._

_Teyla has sworn her allegiance to me. Like she actually cut her hand and did a blood oath to prove that she's willing to die under my orders if it means her people will be safe… I'm glad she's sticking around since we're gonna need all the help we can get. But hopefully next time someone joins up I don't have to clean the floor of my office._

_We need to start trading, and preparing for a long term stay in Pegasus, this planet we're calling "New Lantea" is off the main gate grid so we should be safe from the Wraith and Replicators, as well as those pesky Genii._

_It'll be awhile before we can even think of going back to Earth. There's too many problems in this galaxy anyways to even consider it. At the worst we're stranded, and have to survive on our own, which we were doing already anyways. And at the best… Teyla says she's heard of other groups of people who resist against the Wraith and might be willing to ally with us._

_We're going to one of those places in 2 days… Sateda… Hopefully we can get some kind of trade going with them._

_This is Brigadier General John Sheppard… wow… that'll never get old… signing out."_

* * *

John felt sick, the realization of what had transpired differently here than in his own reality… and the disturbing similarities was hard to cope with. Liz was still taken by the Replicators… Ford was still badly hurt during the siege… and Lorne had decided to stay. He still didn't know what had happened to Teyla or if he'd ever even met Ronon on Sateda… He began to understand why Sam was here, in his room, but seeing the large number of logs left, and the heavy weight of his eyelids, John decided it could wait till tomorrow.

He took off the headset, turned the computer off, and mentally prepared himself to talk to this alternate Sam. The lights were still off, and he kept them off even as he moved into the next room.

The darkness obscured it, he'd never seen a room like this in Atlantis before. John's eyes slowly adjusted to the lack of artificial light and he could make out Sam sitting on a chair a few feet away… next to a carriage she softly rocked. He couldn't help his throat clenching as he gasped. "Oh my…"

Sam turned and shushed him softly. She made a motion for him to stop when John went for the light switch. She was still sniffling softly and waved him closer. Her voice was barely above a whisper, just enough for him to hear. "John… did you see all the logs?"

John moved closer already feeling the lead weight in his stomach do flip flops. She seemed so perfect sitting there, gently rocking the crib back and forth… back and forth... "No, I uh… I stopped after the one where… where I talk about the raid on the SGC."

Sam took a deep breath to control herself. "So… you don't know about Evie."

John finally stood over the crib, and felt Sam's hand wrap around his waist, her head on his stomach. The little baby girl in the crib was sleeping soundly, a tuft of dirty blonde hair covering her tiny head. "Oh my sweet god… she looks just like you."

John knelt down, getting on his knees to inspect the child closely. Sam shifted her head onto his shoulder and held him tightly. "She's got your smile, and your innate ability of getting into trouble." Sam giggled softly as she whispered, the first sign that maybe she was happy.

John was shell-shocked; he couldn't completely register exactly who it was sleeping beneath his face. "This… this is our daughter?" He looked at the baby intently; he could see the mixture of himself and her in the chubby little face.

Sam rubbed his side, and whispered softly. "Almost a year old… our little miracle."

John still didn't completely understand. "Miracle?"

Sam pulled him away; he resisted for a moment, but then let himself be tugged like a disinterested mule back into the bedroom. Once she closed the door she looked at John in the darkness with her shining moist eyes. John couldn't help but notice how beautiful she actually was. "Yeah, she is a miracle." Her face shone with the smile he'd always secretly enjoyed, but only for a moment. "John, I'm sorry I freaked out earlier. Carson told me you were suffering some memory loss but, I guess I just didn't want to think about how bad it might be."

She moved in and hugged him tightly, way too tightly for anything platonic. He could feel her body pressing up against his, and despite all the confusion, all the downright insanity of the situation, he couldn't help but feel right. "Hey, it's ok. You have nothing to apologize for, if anything I'm sorry… I… I should have asked earlier if..."

Sam pulled him along again, and sat him down on the bed. "It's okay John… I'll help you through this. You don't have to rush into this… we should be okay without you for a few days…"

John couldn't take much more of this, he wanted to just tell Sam that he wasn't her John, that this was all completely new to him and he had no clue what kind of state Atlantis was in. But as he looked into her eyes, the pain hidden behind the joy of being with him and their… daughter… He couldn't bring himself to do it. Sam seemed so fragile that the thought that the man she had had a child with was gone seemed like too much a wound to give. "Yeah, I just… I'll watch the rest of my logs tomorrow and you can help me remember what's happened."

Sam nodded and brought her lips to his. Her tongue penetrated his lips and began to softly caress his own. A moment's hesitation and he returned the movements. John hadn't kissed anyone like this in quite some time, and he could feel the heat in her body as she unflinchingly pressed her body into his. Her hands slithered down into the back of his pants, and pulled the T-shirt he wore up and over his head. "I'll take care of you John."

John shivered, here was Samantha Carter, his old boss and most probable wife to General O'Neill in his own reality… undoing his belt and kissing his neck. All John could push himself to do was kiss her back, and rub her lower back with his hands as she began to tug his pants down. If news of this ever made it back to his reality, he was sure O'Neill would come down on him like a bag of hammers.

He contemplated praying for a miracle, since he didn't know if he'd be mentally ready for what this Sam wanted to do, and felt a sickening sense of relief at the sound of a baby crying. "Oh, I think..."

Sam stopped her exploration of his body, and sighed softly. "Yeah, I was hoping she'd stay asleep. I'll take care of her, go to bed John."

John thought about doing what she said, just sitting back and going to sleep. But now the sounds of his daughter… because she really was his daughter wasn't she? The same DNA, the same smile as Sam had said; so he shook his head and put his arms around Sam. "It's ok, I'll help – She's my daughter too."

Sam smiled, and made a soft noise of contentment; they got up together and walked into the next room to sooth the crying baby. John was at a loss as what to do. He'd babysat his reality's Torren a few times, but each time usually ended with him, Rodney and Ronon creating an unholy conflagration of chaos worthy of being called stoogely. John kept his arm around Sam as she picked up the child and gently rocked her back and forth.

All he knew right now was that even though this wasn't his reality, he could feel the sense of family with the people here. After watching the logs, the only thing he really found completely disturbing was their treatment of Rodney, even in his unbelievably frail state.

John was amazed at how maternal Sam was being, within minutes she had soothed the baby's cries, and with a little more comforting pats and rubs of Evie's belly, she fell asleep again. Sam set the child back down in the crib and rocked it back and forth again, watching the small child sleep washed away any stress John felt.

A few minutes later, John pulled Sam away from the baby, and getting back into bed, tried to keep his breathing and pulse under control as she cuddled up to him. Tomorrow would bring more information and with any luck, McKay would figure out how to get them back home, their home.

* * *

Evie had woken them up twice during the night, and John had finally begun to accept that he'd had a child with Sam, or more accurately his counterpart had. The nanites in his body kept him going though, and despite feeling tired, he now felt a bit more alert as he shaved… or rather trimmed his beard to keep the illusion that he was who he said he was. A knock at the door when he finished brought him out in his bathrobe. "Who is it?"

_"__It's Beckett! Get some pants on lad! I got no desire to see your bare ass anymore than I already have to! Least of all in the bright of the morning!"_

John couldn't help but chuckle, and checked to make sure Sam was decent as well. He opened the door and saw the smiling doctor waiting with a small bag. "You make house calls now Doc?"

Carson laughed softly, and moved into the room without hesitation. "Just here to give the whole clan a check up. I'm hoping the wee ones have fixed you up a bit, 'else we'll have to figure out some other way of jogging your memory."

Sam had moved into the other room to pick up the baby, and John had a few seconds alone with Carson. "You could have told me I was married, with a _baby_ in my room. I was in here for almost an hour before I even saw them."

Carson lost most of his smile, and got the caring apologetic look John was so used to seeing. "Aye lad, you'll have to forgive me for that. Usually the babysitter would stay until you came back but I asked her to leave before you arrived so you could have some privacy. It's usually been rather simple to treat you what with the little guys doing such a fine job." He set his bag down and pulled out a scanner. "If you don't mind? I'd like to see how they're doing."

John shrugged and stayed still, he felt a strange tingling sensation as the scanner's beam interacted with the nanites flowing through his veins. "Uhh, I'm guessing it's normal for me to itch while you're doing this?"

Carson nodded, and cocked an eyebrow at the readings "Aye, it's strange… the nanites don't seem to be in any sort of repair mode. I'd have thought they'd try and repair whatever damage is blockin' your memory. I guess Sam and… _McKay_… will have a bit of a day figuring out what happened."

Again, Carson didn't like even having to say Rodney's name. John wanted to ask what the matter was but Sam entered the room, and Carson quickly changed his attention as Sam smiled and spoke. "Good morning Carson, say hi Evelyn!" Sam grabbed the hand of the babbling baby, and waved it for her towards Carson.

Carson chuckled and moved forward to shake the baby's hand. "Well hello there little lass! How's our little troublemaker today?" the baby giggled, almost as if she understood what the smiling doctor was saying. "Sam, everything alright?"

Sam nodded, and sighed with a bit of dejection. "Yeah, You uhh… you didn't tell me how bad John's…"

Carson turned back to John, and sighed with his apologetic nature. "Aye… like I was just telling the General, I was hoping the nanites would fix whatever was ailing him, and I could keep from worrying you both more than necessary. But something else is up… so… I'm sorry Sam, but I'm gonna have to ask you to…"

Sam instantly became defensive, and looking away from Carson sounded bitter. "No! I'm not working with him! He can send me his data through the network but he's not coming within the same floor as me!"

John furrowed his brow. "Hmm? What's that about?"

Sam drew in a sharp breath, and her jaw quivered in rage. "Look John, I can understand why you kept him around, but don't expect me to just forgive him like that. Have him send me any data he gets and I'll do whatever I can for you. But I'm not seeing him again… _ever_."

John palmed his face and dropped his head. "I'm… not gonna like this am I?"

Sam sniffled again, another memory John didn't know about… and it seemed to hurt her to realize he'd have to listen to it again. "Carson, do me a favor and tell him. I'm gonna take care of Evie and Kevin with Lindsay today."

John might have heard it, but was still confused. "Uhh… Carson, I think we're gonna have to have a nice long talk today."

* * *

John didn't believe it. Rodney would never do that. "You are not serious. That's not the Rodney I know."

They were in John's office, all the doors were locked and the blinds closed. Carson had spent the last hour and a half telling John of all the differences in crew, how without the chance of returning to earth, people started pairing off since most of their loved ones were 3 million light years away. Carson had told John with a smile the way he'd announced over the PA one day that all military rules about fraternization were completely and emphatically flushed down the toilet – after standing in for a nice wipe.

Lorne had begun a family with Lindsay Novak, and Carson himself was dating a marine trained Air Force explosives expert, Captain Laura Cadman. Many others had paired off, but almost none of them had tied the knot like John and Sam had. In fact, as far as Carson was telling him, there were only 2 children on the entire base. John's daughter Evie, and Lorne's son Kevin, Kevin being named after a fallen friend. That didn't mean more weren't coming.

That was painful to listen to, Kevin Marks, a good friend of John in his own reality, a top quality pilot and gunner, and a man able to multitask like none other, had been killed by Steven Caldwell in the attempt to take over Daedalus. Marks had just seen the true orders the Daedalus had, and had turned to ask Caldwell whether such orders were truth when Caldwell had shot him point blank. Caldwell himself was later killed in a gunfight with Lorne.

In fact many of the people who John had come to support and expect to be there for him were gone, or had never even arrived on Atlantis. Jennifer Keller was a name that no one had ever heard, and Woolsey was just some political pawn in O'Neill's regime. It had all seemed so strange, yet somewhat believable until John asked about McKay.

Carson was telling him what made everybody hate Rodney despite his genius. "I know you were close to the man, and I even understand how you can look past it for our own good. But I'm not sorry he's dying, and I know Sam ain't either."

John felt his breakfast start to come back up, and keeled over from the shock. He held his stomach as he took short ragged breaths. "How did it… how did it happen?"

Carson sighed, and kept his voice low. "He'd been trying to make her feel better. Took her off-world a few times and tried to help her forget. He… he got drunk one night and tried to make his move."

John swallowed, more to keep his stomach to himself that anything else. "What happened?" He looked to Carson who noticed the rage in John's eyes. "Well don't just sit there, tell me!"

Carson smacked his lips, and leaned forward. "She was working on something in her lab, he came in and tried to get her to have a go with him. She'd… sorta been with you for a few months by then and he couldn't take a clue. The two of you were keeping it a secret. I don't really know why, you'd have to ask her. He tried to force her to go with him and they got into a fight." John kept quiet, and silently reminded himself that this wasn't his reality, and his Rodney would never have done such a despicable thing. "He got the drop on her since she wasn't expecting anything, but before he could do anything, Major Ford walked in on them and well, let's just say I let Rodney heal naturally to that one."

John rubbed his face hard, this was the most disturbing thing he'd ever heard. "Is that where he got the…?" he motioned with his index finger along his face.

Carson caught on quickly. "The scars? Nay, Ford smacked him up something harsh, but the scars were you, you lost your temper and well, you're not exactly the kind of man to piss off especially in those circumstances. When you were done, you told me to keep him alive, because we needed his intelligence if we were going to survive, but leave the scars to remind him of what he'd done.

"I told you then, and even though I've changed me mind I'll tell you again. I wanted to airlock the bastard. Or leave him on a planet with no DHD. But he's pulled a few rabbits out of his arse since… so I don't question your decision, sir."

John kept his breaths short, and he felt like crying. _'This isn't my world and this isn't my Rodney… Damnit… goddamn…'_ "How'd she take it?"

It was a rhetorical question, but one he still wanted the details to. Carson sighed again, the sad nature of the information getting to him. "She almost killed him. The two of you were together by then, and well… you talked her down. I don't know what you said, but whatever it was, it wasn't too much longer after that you both had your rings made." Carson sighed again, as if remembering. "He was my best friend General. And I didn't see it coming. I failed him, I failed you and I most definitely failed her."

John sort of understood why Carson hated the McKay of this universe so much now. An action like that, especially after what John learned everybody on this base had been through would be a harsh betrayal. This reality was so different, almost as if the thoughts and actions of everyone were amplified and darkened. He played with the ring on the chain around his neck and sighed. "When was that?"

Carson furrowed his brow, and cocked his head. "Ohh, bout a year and change after we took over. 2 years since in a few weeks. The Wraith were trying to hunt us down and he was getting really depressed. I know Katie's been taking care of him, and she still believes it was the wine that made him do it… but we were all here for him, and the poor lass had been through enough already. You really did keep her from losing her mind. I think your logs may say more on that than what I know though."

John unclenched his fist – when had he curled them? He saw his fingernails had cut into the palms of his hands, the cuts which now healed over quickly as the nanites did their duty. "Yeah, I'm not done reviewing them. Maybe I should and see what the hell I was thinking before I go and break his…"

John caught himself. Did he really just say he would go and shatter the bones of such a frail looking person? This was more that just trying to go native – something was pushing him to become more like the man he saw in his logs than retain his own beliefs, and if it was affecting him, it was most likely affecting McKay as well. He shook off the ire and looked to Carson who seemed to agree with his rough attitude. "I wouldn't stop you, sir. Breaking him I mean. But I do suggest you watch the rest of your logs, from what you've told me, you make a lot of em."

John nodded, and decided that he needed to talk to Rodney, _now_. "I think I might just do that. Thanks Doc… I get the feeling this is just one of many I owe you."

Carson changed from his serious expression to a weak smile. "Aye, but I reckon I owe you more. I'll be in me lab all day if you need anything sir."

John swallowed his rage, and nodded to Carson as he stood. "Thanks Doc, I will."

He watched as the Scottish doctor left the room, and left him alone to his thoughts. This reality was harsh, this reality was cruel. The people weren't the ones he'd become family to, and the family that waited for him in his quarters weren't his.

_'__Rodney… now.'_

John got up quickly, and stormed out of his office. He looked to where Lorne was sitting at a computer panel and going over what looked to be munitions inventories. "Colonel, I don't suppose you know where Dr, McKay is?"

Lorne narrowed his eyes, feeling contemptuous at the name. "No sir, but I can track him down." Lorne opened a new program, and the city began to scan itself, he turned back to John. "You feeling any better, sir?"

John shook his head, and sighed. "Well, I feel fine, but I still don't remember jack squat. I've been reviewing my logs and Carson's been walking me through… certain events." John had a hard time repressing his rage. "I'm still not fully caught up, so I might need your help in getting completely up to speed."

Lorne nodded, and finally got a reply on his computer screen. "No problem, sir. We still have another 2 days before Daedalus comes back, I'll find some time to bring you up to date on our situation."

John raised an eyebrow, something he'd picked up from Weir. "Situation?"

Lorne nodded, and after pointing on the screen where McKay was, switched to a tactical overview of Atlantis. "Yes sir. Here's McKay in his lab, and about our projects…" He turned to John and gave him a slightly worried look. "Perhaps you should get caught up on what's happened in the past few years sir. We're a long way from what we started out with."

John grunted, but conceded the logic of it. "Alright… If you think that's best. Thanks again Colonel."

Lorne nodded, and gave John the same look of familiarity John's own Lorne often gave him. "No problem, sir. Get well."

John hid his surprise, it was the exact same look his own Lorne gave him when they showed the camaraderie they had. He quickly moved off, and found himself rubbing his chin with the neatly trimmed beard. Absentmindedly thinking what the hell possessed his counterpart here to wear such a ridiculous feature.

He moved through the corridors quickly, soon noticing things were very different than the Atlantis he'd come to know as home. Many of the balconies had been sealed off with airtight pressure plates, and those that weren't had heavy gun emplacements attached. Heavy gauge wires flowed all over the place, sending power to gods knew where.

Dozens of people walked by, almost none of them in typical Atlantis BDU's. A mixture of Traveler style clothes and a militaristic uniform were the predominant fashion. He recognized some of the people, but most were unknown Atlantis personnel he rarely interacted with. He'd noted earlier that on his computer was a complete list of crew assignments and bios… he'd have to take a look at those if he was going to be here for awhile. He saluted them all out of respect, and since they all gave him their distance.

It wasn't long before John reached Rodney's lab, which was devoid of the typical dozen or so scientists he'd no doubt be berating for any odd reason. Instead of finding him hunched over a tablet with a coffee mug on the table next to a ham sandwich, he found Rodney sitting and staring out into space – almost as if he were contemplating.

John found it difficult not to draw his sidearm and shoot the man. The bitter taste of what this reality's Rodney had done tugged hard on him, and he had to actively remind himself this wasn't the same man. "Rodney…"

Rodney turned, his face stoic and contemplated. "Sheppard… I've been waiting for you. There's a lot we need to talk about."

John fought to keep his voice calm, but the rage boiling in his veins showed in his clenched fists. "I'll say we do. Do you have any clue what your evil twin bastard did here?"

Rodney's face showed he didn't. "No... no one will talk to me. Even Katie won't tell me why. As soon as you walked away we started fighting. All I can access in the computer is my research. I don't even have any logs." He had a defeated expression on his face, almost as if he welcomed Sheppard's wrath.

John was willing to give it, and forced himself to back off, the strange pull begging him to act was overpowering, and he knew that if he didn't put some distance between them and his emotions, he'd most likely cave Rodney's face in. "You wanna know why? You really wanna know why everybody in this place would love to put a bullet in you?"

Rodney nodded, and looked to John with a gaze that showed his resignation. "No, but I have to know. I have to know what I did – why you've got a gun to my face."

John opened his eyes wide in shock – he hadn't even realized his right hand had already drawn the Sig Sauer P229. it shakily pointed at Rodney's head and John fought the intolerable urge to pull the trigger. At this range, the .357 SIG wouldn't leave much behind that could be called a head. He felt beads of sweat roll down his temple, and the vibration as his mind fought his body. "You… _you…"_

Rodney stared down the barrel, and John could see in his eyes that Rodney was ready to die, ready to pay the price for what his counterpart had done. "Yes…"

John bit his lip hard enough to draw blood; his mind was screaming to stop but his finger began to put pressure on the trigger, pushing the firing pin back millimeter by millimeter. Rodney closed his eyes and embraced the moment.

With a sudden scream of effort, John used his other hand to slap away the gun, it fired into the floor, digging into the alloy floor and sending up a loud spark. He dropped the pistol and felt the sudden release of tension, his senses finally coming back to him. John drew quick rapid breaths, falling to his palms on the table in front of him. Rodney cried, and keeled over on the desk sobbing uncontrollably.

A pair of marines whom John didn't recognize entered the lab with their weapons drawn, They quickly moved behind cover and screamed. "General! What happened?"

John was still in shock over nearly shooting his best friend. He turned to the soldiers and kept his voice low. "Get out."

The marines moved in quickly, securing the area and grabbing the loaded pistol on the ground. "Sir, we heard gunfire! Are you alright?"

John didn't like having to repeat himself, even in his own reality. The callous tone he used frightened even him as he used it. "I said get out! _Now_! Clear the area! Wait for my orders!" He snatched the gun back from the marines and holstered it, surprised at the violence of his movements.

The marines looked at each other, but then nodded and moved out. They got on their radios and soon John and Rodney were left completely alone. John looked to Rodney and kept his voice quiet. "The hell's happening to us Rodney…?"

Rodney sobbed, and as he drew short ragged breaths he tried to make sense of it. "I don't know Sheppard. I… It must have something to do with the body swapping. We've got our memories, but these bodies are used to a certain pattern, and that pattern is influencing us." He sat up, and using his cane to push himself along on the wheeled chair, sat in front of John. "I know I did something, something terrible. I've got the distinct feeling I should pay for it, but I think that's what the other Rodney thinks. He was ready to die and now I'm feeling the same."

John sighed even as his body quivered. He needed to tell Rodney what he'd discovered. "Rodney, the other Rodney… the one you say is ready to die…" he was silent for a moment, trying to build up the courage to say it. "…he tried to rape Sam." His tone went from a somewhat calm one, to a harsh and unsympathetic one.

Rodney drew in a short hard breath, and began to cough. His breathing struggled for a few moments until he finally stopped. His eyes watered uncontrollably and his voice cracked with sobs. "Oh my, _Sam?_ She's on the base? I… I didn't… I've got… I have no clue about anything in this place! I… I mean… he tried to…?"

John felt the tears build up in his eyes too, but deep breaths, and the meditative techniques he'd learned from Teer helped to control his emotions. "Yes Rodney… that's why everybody hates you here."

Rodney leaned on the table, and was silent as he tried to fathom what happened. John kept silent as well, neither really knowing what to say. Finally, more out of needing to reassure himself than his friend. John spoke softly. "I know it wasn't you Rodney. I know you'd never do that. But this place is different. My logs are telling me how bad this place has gotten."

John stopped, Rodney needed to be his first concern, not the state of politics in this reality. Rodney sniffled, and wiped his eyes. "I'm dying Sheppard, I know Carson said a month but you can't imagine how bad the pain is. I can't even think straight. Katie has to help me with everything."

"Come on, what happened to the 'I'm always right' Rodney? You've gotta have some idea how to get us back!"

Rodney shook his head, and sighed heavily as he dabbed at his eyes. "I can't Sheppard, it's just too much. I was up all night thinking about it and there's only one way I can think of."

"What is it?"

Rodney palmed his face and sobbed softly. "We need to examine the Jumper, investigate that storm, and do a whole series of tests… the only problem is I'll be dead by the time we can replicate it, and the best person who I think might be able to help us would never help me here."

John winced as the realization hit. "You don't mean…"

Rodney nodded, his tone a quip. "Yep. I was hoping Zelenka could help but evidently he's not on Atlantis, he's with the Travelers teaching them.

John rubbed his eyes hard, he had to tell Rodney everything. "For the love of God Rodney, You don't even know why Sam's here…"

Rodney shook his head, but didn't face John. "No…. but I guess it's not good."

"Long story short, Jack O'Neill is insane and took over the SGC as well as Earth, He's using some weird Goa'uld sarcophagus thing, and it's affecting his mind. He sent everybody who had the ATA gene naturally here to Atlantis to get as much technology as possible before sending Daedalus a year later to kill us all. I didn't take too kindly to that and took over. We nuked the SGC in a raid and rescued Sam from him."

Rodney furrowed his brow, not understanding. "What? Rescued? Nuked? What the hell happened?"

John found himself feeling revolted again. It hadn't been him who broke down that door in the SGC, but the way he was feeling he figured it might as well have been. "O'Neill had her locked up in his private room for…" John couldn't finish and clenched his jaw.

Rodney on the other hand coughed once more, fighting back retching while John slowly told him everything that happened with just his movements. Having it all dropped on him like a bag of hammers was obviously not supportive of his mental and physical health. "Oh you're not serious… _O'Neill?_ Those two are like soul mates back in our reality!"

John nodded, and sighed. "Don't I know it, and… you said these bodies are used to a pattern right?"

Rodney sniffled again, and winced from some unseen pain. "Yeah, I guess that's why I'm bawling like a toddler."

John clenched his eyes shut, and tried to make it as simple as possible. "Well, I think I know why I feel like I hate you. I'm _married_ to Sam in this reality."

Rodney looked at John again, a mixture of shock, betrayal, and confusion. "What! But… how…? You know I…! Your evil bearded twin would have known…"

John huffed in amusement, at least the Rodney he knew was still somewhere inside this broken husk that sat before him. "We even have a daughter… I… I'm not sure of all the facts yet. I'm not too sure I want to know. So you might understand why I'm feeling reluctant to ask her to work with you."

Rodney nodded, and collected himself to speak. "I… I know… But she's the only hope I have Sheppard. The only chance I have of surviving long enough for her to figure it out is if you put me in stasis, and let her work on her own with the data from the jumper."

John sighed. "Yeah… I'm just not sure if can bring myself to ask her."


	3. Bargaining

**- Chapter 3 - Bargaining- **

John sat on the bed in his quarters, he didn't have a clue how he was going to broach this, but seeing as how neither he nor Rodney really were from this reality, he didn't see that he had another choice. He contemplated watching more logs, but procrastinated so he could have a few moments with only his thoughts.

Sam was gone, off on a play date with Lindsay Novak and the kids. _'__God'_ he thought. _'__I have a daughter with Samantha Carter.' _The idea was finally beginning to really sink in. and he harshly fought down the sudden almost imperceptible urge to want to stay. Rodney was dying, his best friend was dying, the same best friend that had tried to …

John closed his eyes and winced. _'__No!'_ He thought. _'Not Rodney… not the one I know… Dammit get out of my head you bastard!'_ He didn't know who he screamed at, maybe he just wanted to prove to himself that this wasn't what he really thought. John finally worked up the courage to turn on the computer again and take a look at the logs he'd, or rather, his counterpart had made.

* * *

**New Atlantis Log – Day 14**

_"__Sateda turned out to be a mostly dead end… except for a few survivors, that planet has been utterly destroyed by the Wraith. The leader of the survivors, big guy, calls himself Ronon Dex. He said he'd join us if we fight the Wraith,_

_Lorne wasn't too sure about him, but I had a long chat with him while Grodin, Teyla and Beckett dealt with trade and medical stuff. He's got a lot of pent up rage… I guess I can relate. He's been fighting the Wraith for as long as he can remember and he's lost everything to them. When I told him we were looking for allies in our fight against both them and the Replicators, he said he'd think about it._

_That is until I told him about my personal fight with O'Neill. I guess he saw us as two sides of the same coin and decided to join us._

_I'll admit, it's a little intimidating to have 20 of the best soldiers that planet created training with my men, but he's as good if not better than Teyla with the Banto sticks and he certainly whupped my ass in a sparring session, even with the nanites._

_After some comparing, his squad is comparable to our own Special Forces. They're quiet, deadly, and very efficient. They're also fanatical so I've decided to give them a wide berth from the civilians left on base. They hate the wraith with a passion, and I think that'll come in handy eventually._

_Teyla herself seems to be able to talk to Ronon more effectively, and somehow, she won't tell me exactly, she managed to get Ronon to devote all the resources his planet had left to Atlantis. From what McKay says, their weapons are about 50 years behind us technology-wise, but still effective against the Wraith. I'm just glad we have more ammo stores so we don't burn through our 5.7 so fast._

_We were worried about food for a bit, especially since it's not just our people we're dealing with now, the Athosians and Satedans bring our population count to a little more than 300, and the city's still not even a twentieth full. There's still a million and a half rooms to explore and we're having to deal with all the crazy shit the Ancients left._

_I'm reminded of what Napoleon once said. "The biggest problem a General faces is not defeating his enemy, but feeding so many troops and horses." Or something along those lines. My problem is my troops EAT like horses, and while I don't have any beasts of burden, McKay certainly makes up for any equine pets I might want to have._

_The Athosians have talked about heading to the mainland to start farming, and I'm seriously considering it, the only problem would be in an emergency, they'd be defenseless without our shields or weapons. Halling is pretty adamant about going though, and in the end if he really does want to go, I won't get in his way._

_Sam's been… well she's slowly coming around. She doesn't cry as much, but she still wakes me up at night sometimes… when that happens well… This is the last thing I needed, but I guess I gotta live with my decisions. McKay's been trying to help too but I don't think she wants it from him. Neither wants to tell me what happened between them back in the SGC, and to be honest I can't care right now, even though I want to. Sam's serving as my XO for right now as she was a full bird Colonel when we… liberated her and Lorne's on Daedalus. Since she has a strong science background, she's taking over what Weir was doing and keeping an eye on the civilians and non-military side._

_We're still checking gate addresses, and even though we're not officially a part of Earth's government, we're still out there exploring and meeting new cultures. Keeping trade, cultural, and social connections is more Teyla's side of things, and she's always ready to help me. I've got too much on my mind what with trying to make sure every metaphorical horse in this place is fed and we've got enough energy to keep going._

_On that note, Rodney's found more Ancient labs in the database, I'm putting Ford and Stackhouse in charge of Off-World operations, as well as Teyla and Ronon to give them some cultural backup. I'm reluctant to send them off… but I guess that's what being a General is all about isn't it?_

_I've decided to make this a regular thing… unless something comes up that I want to have a reference for I'll be making these logs every so often… although it's not like I get days off. That stuff always fell to Weir and Sumner back when… well back when things were simple, even as complicated as they were. I've got so much work to do now, and surprisingly Sam's being a good help, taking over most of the at-home science stuff while McKay goes gallivanting off-world._

_I'm… still a little uncomfortable sleeping in the same room as her, so I've talked with her about it and we're going to be moving to Weir's old room, the one with 2 separate bedrooms but still connected. Sam's okay with that as long as me or Lorne are around, From what I can tell she just wants someone she trusts nearby._

_Speaking about Lorne, I've promoted him to Lieutenant Colonel. I know it's not official with Earth or whatever… but he's got command of the only real capital ship we've got and he deserves it, we wouldn't be here if it weren't for him. Ford's doing alright now and I've promoted him to Major, and Stackhouse to Captain along with Cadman.._

_I've had to make due with the few officers left, and I'm considering giving Ronon a field commission. He is military trained, and from what I can see, as long as it matches his goals, he'll take orders._

_Goddamn I hate you O'Neill. If trying to kill me wasn't enough, now I've got a whole city to look after. I swear I'm gonna tear your balls out through your ass. And that's just to start._

_Till next time."_

* * *

John sighed, and began the next log. Things looked pretty much as he expected they would go, and if he was right, it wouldn't be long before one of the biggest bangs the Galaxy had ever seen would happen. Log after log eventually led to it.

* * *

**New Atlantis Log – Day 45**

_"McKay finally learned his lesson… I hope. And the worst part is it cost 4 lives… Lorne ended up having to order one of the marines with McKay to stun him and drag them out of the Project Arcturus facility. Daedalus took some damage as well and three quarters of that star system went kaflooey… well… five sixths._

_I don't know what his problem is, he's not talking to me as much anymore and Carson says the same, I know it's been hard having to sever all ties to Earth, especially since he has his sister still back there, but we're all here for him. I've relieved him of duty for a few days so he can relax and think, Sam's offered to take over his duties for awhile but she still refuses to go off-world without either me or Lorne with her._

_Sam's been a bit of a puzzle, no scratch that, she's driving me completely insane! It's strange really. I solved a rubix cube when I was still in grade school, but this woman is like a freaking Gordian knot! She refuses her own quarters, won't leave my side if it's her choice, and she still won't tell me much about her time with O'Neill… though…I guess I can understand that last one, the bastard did hurt her. But she's safe now and he's not going to be able to get to her easily. He's got the threat of the Ori looming over the Milky Way so he can't do jack about us without leaving a big open gap in his 'empire'._

_From what Sam HAS told me though, if the Ori beat him, we won't necessarily be any better off. So I've talked it over with Sam, Lorne, Beckett and McKay and we all agree that we're going to leave the Milky Way on it's own unless Earth comes under direct attack. It might not be home anymore… but that doesn't mean we still don't care._

_Atlantis's rearming is going along smoothly, but we're running out of resources to build. Sam and McKay have been working on the problem, and they've been thinking of using the Daedalus's beaming technology as a mining tool. It's a little too complicated even for me so I can only imagine what was going through Lorne's head when they explained it. I swear, sometimes those two can bounce ideas off each other and talk like they're brother and sister…_

_Uhh… on that note. McKay kinda confronted me a few days ago before he set out for Arcturus. He said I should back off of Sam and well… it was a struggle not to laugh. Sam's obviously just as, if not smarter than him and can make her own decisions. Granted, she's taken a bit of an unhealthy liking to waking my ass up in the middle of the night, but can I really be blamed for that? 'Sides, she needs time, and I'm not touching that issue with a ten foot pole till she's ready._

_I gave Carson a few days off as well so he could go with McKay somewhere, most likely the new Athosian settlement on the mainland. We need everybody frosty and after Arcturus… I think McKay needs to unwind a bit. Thank God Carson is such a comedian or else I'd probably have riddled McKay with bullets by now._

_Not that he's all that bad… he's pulled our asses out of the fire enough times. Ford and me have been getting chummy with him to try and get his mind off things and well… despite basketball being Canadian he's not that good at it. Doesn't matter, it's helping._

_Ronon and Teyla seem to be getting along well *smirk* a lot better than most others I'd say. In fact I'm noticing that… well since we've lost contact with Earth, and we're really the only ones we can trust in this Galaxy, a lot of the guys are starting to compete. Hell with McKay pretty much telling me to lay off of Sam, I can only imagine what everyone else is feeling._

_I don't think we're ready for that sort of thing yet, so the Frat Rules are sticking… at least for now."_

* * *

John sighed, the Project Arcturus mishap in his own reality had only claimed one life. For Rodney to have to deal with his failure… and apparent lack of recognizing that failure to the point where he had to get dragged out by a marine was something he wasn't expecting. In his own reality, John had managed to convince Rodney to evacuate with a pilot story about crashing and burning for no reason other than stubbornness. It was apparent that the Rodney of this reality hadn't learned that lesson fully. The next log was almost a month after. Despite being in his personal folder, it had a different encoding. Someone else had written it.

He tapped it open and wasn't too surprised to see Sam's face staring back at him, her hair looking odd in a barrette instead of her typical ponytail. She seemed a bit sad, but more confused than anything else.

* * *

**New Atlantis Log – Day 73**

_"__This is Colonel Samantha Carter, acting commander of the Atlantis Expedition. I'm uhh… I know you usually keep a log of what's going on John. I also know you've been too busy to make one in a few weeks and well, you're not exactly in a good condition to make one now._

_About 2 weeks ago we came into contact with a scientist who said he had developed a serum that could suppress the Wraith feeding urge. The village he was in begged us to help them hunt down a Wraith that was hunting them and suspected him. He had a little wraith girl that he'd raised as a human… and for a while we assumed it was her. But it turned out there was another Wraith there as well, and for a few days we were hopeful the serum was working. You and I along with Teyla and Ronon and Doctor Beckett stuck around to see if it was true._

_Carson did some testing, and it became apparent that it was pretty much useless, but it turned out that Carson had been working on a retrovirus that was supposed to suppress the Wraith DNA and convert them into Humans. The little girl, Ellia, she was so desperate to be human that she took the virus before Carson could test to see if it was ready…"_

* * *

John felt the pain she hid, and her body posture and facial expression belied how bothered she was by what happened next.

* * *

_"… __It did the exact opposite. She turned into a giant bug creature and escaped the cave Zaddik had her in. Me and Doctor Beckett were out looking for the other Wraith when we got ambushed by it. I managed to kill it before it could feed on us, but when Ellia showed up… she attacked us._

_You and Ronon were right behind her, and she seemed half lucid. You got her attention off of me and tried to talk her down, she let go of me and went after you._

_She fed on you John. Only for a second or two since we all opened fire. But even with the nanites it really put you out._

_Carson was worried when you didn't just regenerate right away, but by the time we got back to Atlantis you were feeling a lot better and the wound had healed. He said the nannies probably learned how to counter the feeding process but wasn't eager to test that theory, 't least that's what we thought._

_About a week later, we were in the gym. You were teaching me some sparring moves and well… you kinda lost control…"_

* * *

John winced in sudden embarrassment, remembering the event in his own reality. It had been real awkward with Teyla for a few days after that – If he'd done the same to Sam…

* * *

_"__You umm… you kicked my ass John, it was… weird. Usually you win by default just 'cause I'm still learning, but this time you – well you didn't hurt me but you just, you pinned me to wall and… you kissed me._

_I didn't know what to do, I still don't know what to think! But it didn't matter since you sorta freaked out, then backed off. You kept apologizing but, I dunno. You had this look in your eyes… I was worried about you and we went to see Carson. That's when it started happening._

_The retrovirus Carson had given to Ellia passed into you when she fed on you along with her DNA. It turns out that the Wraith DNA is resistant to the nanites and it took a few days for the effects to become noticeable._

_Right now, at this moment you're in the infirmary, and we're trying to find an Iratus bug nest to get the stem cells we need to help you. It's dangerous, but both me and Lorne agree we can't lose you._

_I… I haven't told anybody about the gym. I think we need to talk about that in private. I'm… I'm sorry I've been such a burden to you John. I know I've asked a lot from you and… *sigh*"_

* * *

The log ended suddenly, and John winced as he realized what had happened. In his own reality, he'd grown closer to Teyla as they were teammates through the years. But in this reality, he'd grown closer to Sam by being there for her and leading what was left of the expedition. How it had evolved into a marriage was something he still wasn't too sure about.

How was he going to ask her this? How could he ask a women who had already been through so much pain, so much emotional abuse, to help a man who in her mind tried to violate her? For that matter, how had John managed to convince her to let him live, let alone stay on the base?

John had a feeling the next few logs would explain more, as the ones that were there were either very short, or taking place later in that same first year.

* * *

**New Atlantis Log – Day 78**

_"So here I am, de-buggified and hating the Wraith even more than before. As if that damn Iratus bug in my second week here wasn't bad enough._

_Two marines died trying to get the stem cells I needed. I ended up having to go in myself to grab the eggs. At least that's what they tell me. I don't remember too much after Sam brought me to the Infirmary._

_I… had a little talk with Sam. And I watched the Log she made for me. We've agreed that it might be better for her to get her own room for the meantime. I don't blame her and the upside is I might get a good night's sleep for once. Still… she loves hanging out with me when we do get free time. I taught her how to swing a golf club the other day on the south pier. I guess I'm getting used to having her around all the time._

_McKay's ecstatic over it, and I think he asked her out earlier, don't know how that ended up and I think it'd be better if I don't get involved. The strange thing is that I thought he was getting kinda friendly with Dr Brown in botany._

_I can't deal with that stuff, so I'm gonna ignore it for now. It's not manly, and it's not brave, but I've got more important things to worry about, namely Carson trying to convince me to give the retrovirus another try._

_That means we're gonna have to stop hiding, and hit the Wraith hard. Hard enough to come back with some prisoners. Maybe Liz was right, maybe I am really turning into a monster."_

* * *

John didn't really know what to think. It had been awkward enough with Teyla, he could only imagine what it was like for his counterpart, especially with McKay and the entire city to look after.

The next few logs were more of the same, status reports on resource gathering, more personal musings on happenings throughout the city, more mission reports that sounded eerily familiar. The biggest difference was that most of the time, it wasn't him who experienced the events, but rather the new leader of AR-1, Major Ford.

It was incredibly surprising, and even hard to imagine that the young man whom John had long thought to be lost in his own reality, had decided not to ascend with the others in the time dilation field where he himself had spent several months. It was almost disconcerting to think that he never had that experience, that the John Sheppard of this reality didn't get the opportunity to learn calm and meditation. He was hardly expecting anything seriously surprising when the next log made his blood freeze.

* * *

**New Atlantis Log – 232**

_"This… *sigh* this whole month has been completely… I can't even think of a word strong enough._

_We'd finished transferring the drones from that crazy feudal society that had that destroyed Lantean city ship. Lorne's made me swear not to tell anyone about what the one daughter tried to get him to do… and I'm still not sure he didn't do it, but whatever, he needed some stress relief, and since the frat rules are still on… I don't think he's been able to do much with Novak since we're so busy._

_The craziness all started with those damn Escape Pods we found, We brought em back to check them out and when McKay asks Teyla to look at them to see if she recognizes them, wham! She gets zapped by this beam. Turns out it 'imprinted' the lady inside's personality onto her, and all of a sudden Teyla's calling herself Phoebus._

_Seemed harmless enough once she explained it was only temporary, and that the other escape pod had her husband Thalen. She asked me to let it imprint on me so they could spend the last few hours they had together… I uhh… I wasn't exactly thrilled with what might happen especially since Ronon's just looking for another reason to kick my ass, so he ended up biting the bullet._

_Guess we let our guard down, and once they get together, Ronon and Teyla start tongue wrestling. I'll admit, at the time, I thought it was hilarious, I'm like… 'wow, they're finally hooking up and it isn't even really them.' Next thing I know, they're turning my conference room into a shooting gallery with flying knives and bullets all over the place._

_Poor Chuck ends up taking a dive over the railing to avoid one of Teyla's blades and landed right on Zelenka. That was one of the funniest things I've ever seen and if I wasn't running and screaming for reinforcements at the time, I would have howled mercilessly._

_From what we could tell, they had complete control over their bodies, and even their memories, we had a whole Predator Vs Alien theme going as we're trying to hunt them down with stunners._

_It's a complete fucking miracle they didn't kill each other, let alone the rest of us, in total, they ended up taking almost 4 hours to finally tire out enough for us to shoot em down. They're still recovering in the infirmary under Carson's Midas touch._

_As if that insanity on the base wasn't enough, the Genii have decided to go all topsy turvy on us and start a civil war! We had sent Stackhouse's team to investigate a planet we trade with for possible Genii infiltration when they were ambushed. We moved in fast, but by the time we got there it was too late, It looked like the Genii had found them, killed them, and burned them in a farm house._

_At least that's what we thought for awhile, 2 days later, Ladon Radim, the head of Genii military contacts us trying to bargain. He offers us a ZPM in exchange for help in overthrowing Cowen and peace between us. I… this isn't the kind of decision I like doing on my own. I called a conference and we discussed it. I still felt like shoving a nuke up his ass after what he did during the Storm on Lantea last year, but when Carson finally got the results back on the charred remains we found, we realized that Stackhouse's team had been captured, not killed._

_Ladon sent us some people to work out an agreement, but as it turned out they were all suffering from acute radiation poisoning. Thankfully it hadn't reached the point of no return, and once we told Ladon that we could help them, he 'fessed up about the ZPM being useless._

_We sent a strike team to help him in his coup, and Cowen never knew what hit em. His elite guard couldn't really fight off an orbital bombardment, and I myself led the strike team. Cowen died a coward, hiding in his panic room. We ended up just gassing it and leaving him there. And if that wasn't enough. Ladon activated their prototype nuke and wiped that base from existence. Ladon Radim is the new leader of the Genii and despite a group of his army splitting off and going rogue under Sora... that crazy chick that hated me and Teyla, for the most part we now have peace with the Genii. Huh, peace. It's been a long time since I really thought about it, especially in this galaxy._

_With the Genii's help, we tracked down a small Wraith lab in exchange for weapons and technical assistance with their nuclear program. McKay is excited about working with them, but I'm still not sure we should be giving these people the bomb so easily. I've been in and out of meetings for the past week with Ladon and his people and I think he wants to join forces with us officially._

_Back to the lab, we launched a full strike yesterday using the Daedalus and a few jumpers worth of Marines. The Wraith didn't have a chance and we captured what we think is one of their head scientists. Daedalus is bringing him back now since I don't want more than one Wraith on the base at a time. Carson is finally going to get to give his Retrovirus a shot and well… we're all hoping it works._

_That's… not all though. Something happened last night I really wasn't expecting… and I'm… unsure of what to do now._

_Sam's been getting much better, she's been eating more, going out more, and she doesn't seem as nervous as she used to be. We've hung out a lot since we brought her back and well… I guess I should have seen this coming. She's got no problem being on her own anymore, and from what I could tell, her and McKay were sort of 'Non-dating' if you asked her. Of course he figures he'll propose next week but I'm gonna cross that bridge when I get to it._

_I wasn't expecting anything, and I'm still not sure where it came from, but last night around two in the morning she showed up at my quarters… and it looked like she'd been crying for awhile. I didn't really know what to do so I just… I pulled her inside just so no one would see her. She started crying again… and poured it all out to me. I told her she didn't need to rush it but she insisted._

_She told me everything, O'Neill's plans, what he used to be like, and why she thinks he turned into such a monster. She even told me that he thinks I'm the biggest threat to him… because of my Gene._

_As it turns out, when he went on the original Stargate Mission to Abydos, he was killed and revived by Ra several times before he managed to make an escape. That was what broke him, the sarcophagus healing device. She told me about how his family died, and how he lost his mind after going through that process so many times and never having had the chance for his family. It took her and Dr Jackson awhile to figure it out, but by then it was too late, and Jack had his own personal sarcophagus he used every week. They couldn't do anything, since Jack was in command of the SGC, and it wasn't too long before he started acting like the Goa'uld he'd killed not long before._

_Sam said that she always felt something for him, even from the beginning, that she had a taste for the lunatic fringe… but he'd gone too far, he'd passed the fringe and become something she hated._

_So when I broke down that door in the SGC, the best she was hoping for was for me to kill her, and put her out of her misery. When I brought her back, she realized that by being close to me, she'd never have to worry about dealing with O'Neill again, at least not in an amicable way._

_I figured out most of this on my own from what she'd told me before, but there's a lot more. I'm putting that down in an encrypted file, I don't think the others are ready to hear that yet and we're still fighting to survive here on our own. When the time comes to go back to the Milky Way… then we'll open that can of worms._

_What happened last night… *sigh*… after she told me everything… she…she said she didn't want to be alone anymore. I guess I should have seen this coming… I've been… well with everybody pairing off… One thing led to another and well…I haven't had any time to think about sex… especially not since I was infected with these nanites… and ever since Chaya it's really not been that important to me. But Sam needed it… we both did, and before we know it it's fuckin' 4 in the morning and we're still… oh man… this is fucked up._

_At the time I was infected, Carson did an examination, and his findings indicated that I should be… well there shouldn't be any problems if I so chose to, but compatibility was a problem… not that I really cared at the time. Sam's bio showed a protein marker from having been host to a Goa'uld for a few days, and we're not sure if there might be some… complications. Neither of us were thinking straight at the time and now I'm really worried I've fucked things up royal. We agreed to go see Carson later but… I don't know exactly what she thinks., When she left a few hours ago… she was smiling. So I guess maybe we'll be ok._

_I was hoping to finally get rid of the frat rules for Lorne and Novak… but I guess things have a way of piling up on a guy._

_God I wish things were simple again."_

* * *

John couldn't believe it. Lorne had mentioned that O'Neill had changed after the Abydos mission, but Sam's explanation made perfect sense. The realization that the biggest thing that made this reality different to his own was the bad decision of one man chilled John's blood. Everything he saw now, Atlantis in space, and fighting a war with just about everyone... it all stemmed from Jack O'Neill losing his family and bitterly using technology as a crutch.

It was late in the afternoon now, and John was still watching logs to figure out how Atlantis ended up where it was. Michael had been in this reality too, with the exception of being more of a success, and instead of the retrovirus being a dead-end, it was used as a biological weapon against the Wraith. John recalled doing that once… with disastrous results to Carson Beckett and the rest of the galaxy. In this reality it ended up being one of the key weapons against the Wraith. He'd just reached the log that spoke of the Aurora class ship they found in the super volcano facility when the door to his room opened.

Sam entered, and she looked at John with a strange gaze. John didn't really know what to say; now that he knew everything that had happened. So he took the headset off and stared at her, with a look that spoke of his apology.

She moved forward and sat on the bed across from him. Her voice was soft. "I heard what happened today."

John gulped, and nodded as he stared at the floor. "Yeah, I… I can't believe he did that."

Sam sniffled, and wrung her hands together. "Well he did, and you almost killed him…"

"I almost killed him today."

Sam wiped the tear forming in her eye. "I… I don't know what to say John. This was hard enough then, and I'm trying to be patient since I know you don't remember. But, I guess I'm a little relieved that you still act the same."

'_Nearly killing Rodney is my normal modus operandi? Good god.' _John got up out of his seat and sat on the bed next to her. She cuddled into him. John whispered. "Sam… where's Evelyn?"

Sam nuzzled against him, and kept her voice just as low. "Lindsay offered to take care of her… she thinks we need to be alone tonight."

John looked into her eyes, and felt the urge in his heart again.

Sam smiled, and leaned forward to kiss him. "I agree with her."

* * *

John tried to reason with himself, and kept on failing.

Sam lay asleep on his chest, her body limp and relaxed as she cuddled into him. The great feeling of her soft body against his skin was still there, but the clear and imposing feeling of… he didn't even know how to describe it. Regret… stupidity… Lack of control… ?

It'd started out with just cuddling, and the next thing he knew he couldn't control his body anymore. It wasn't like she'd forced him, instead he just couldn't think straight anymore. All he knew was that he wanted to reassure this woman, he wanted to be the man who was supposed to be there.

That nagging feeling was still on his mind though, no matter how much or how correct he knew he was that this was wrong, it kept telling him that it was right.

The memories of last night were burned into his mind. The flutter of images he'd never seen before, but could feel nonetheless. The memories were vivid, Sam's supple skin as their bodies contracted, hearing Sam's laugh when he decided to follow her into the shower, the way Sam embraced him and told him she loved him on their honeymoon…

Wait… What?

John shot up straight, it was high time to be getting up anyway. His mind was completely discombobulated and he took a few seconds to reset his thinking. He didn't even notice Sam flip off him onto the bed, then loudly complain about being woken up in such a crass manner.

He remembered his honeymoon.

"Sam, we honeymooned on that planet with the tropical beaches. We took a week off and a jumper – Lorne gave us the last case of Jose and told me not to drink and fly."

Sam whined, but nodded with a snicker. "Yeah, you didn't listen…" She realized the implication and shot up as well, eyes wide. "Wait… You remember?"

John's genuine confusion served well to protect his alternate reality identity. "I… Yeah, took you two days to fix the Jumper."

Sam gasped and the hint of a smile came to her mouth. "Yeah,... woulda taken only a few hours but we were plastered. Kept having to redo the job." She started chuckling remembering the event. "I guess last night musta knocked some memories loose." A lewd look came to her that John found criminally attractive. "Might have to try this again later."

Her laugh calmed John, but John didn't want to be calm. He wanted to freak out, he wanted to haul ass out of this bed, run out into the hallway, do a quick 180, get back in the room, put at least his pants or a pair of boxers on, finish the 360, and track McKay down for a very serious talk.

But instead he just stayed in bed, awash in a memory that wasn't his. "When we finally got it fixed, we went up into orbit, turned the gravity off and…"

That memory certainly felt good. John was no stranger to odd sexual positions, but sex in zero gravity was something he only wished he could do, James Bond came to mind. Sam giggled, obviously remembering as well. "It was so confusing, I kept on cursing Newton every time you…" She laughed harder, and leaned forward to hug him. "Ohh god… I'm glad it's coming back to you."

John took a moment and closed his eyes, something he'd learned from Teer came in very useful now. Time was relative, thought was instant.

_'__Okay… think John think… You just spent the night fucking Sam Carter in a shower, then on a sink, then in a bed while still soaking wet from said shower and sink. You passed out on top of each other and woke up 2 minutes ago. What the fucking hell were you thinking? You utter **idiot!**  
_

_You remembered images… things you may or may not have seen but most likely haven't…_

_You also remember going on a honeymoon with said Sam Carter even though it wasn't technically you… The memory is clear, hell, you can even taste the Jose on her lips… The question you need to ask is __**how**__ can you remember that…Okay… what is it McKay said? These bodies have a pattern? Okay… line of reasoning, What is memory… uhh… okay, first… no wait, second on to-do list. Ask Carson what Memory is. First is talk to McKay and see if he's feeling the same."_

Sam's ran her fingers through her hair, and quietly cursed as they got caught in the tangle. It only took John a moment to go through his thoughts and look down at Sam, Without any real reason, and more out of instinct he asked. "Sam… when did we do this last?"

Sam tugged on her hair, and gave John a lewd smile. "Umm… bout a month ago? We've been too busy and Evie's always a handful." She smirked again, and this time lifted up off the bed stretching her arms and shoulders.

John couldn't help but notice how beautiful her naked back was. "I get the feeling we don't get much free time."

Sam turned back, even as she stood up. "Part of the job. then again you're the one who told me that."

John raised an eyebrow, and thought carefully. "I did say that didn't I?"

Sam furrowed her brow, and sighed softly. "Guess we only jarred a few memories – figures it's our honeymoon." She laughed as she began to walk to the bathroom. "I'm taking a shower – and no, you can't join in this time. I feel like a piñata."

John silently ignored her laughter, again lost in thought. For what seemed yet another time, his thoughts said one thing loud and clearly. 'Rodney… NOW.'

* * *

"Oh great, you're having wild jungle shower sex with the most beautiful woman I've ever known and Katie bitches at me like I've never seen before when she has to help me get into the tub! That's the fairness of the universe for you!"

John ignored Rodney's typical, albeit hilarious snark, and despite feeling an even greater sense of hostility towards him, was able to consciously put it out of his thoughts. "_McKay!_ Did you even hear me? I'm remembering things that never happened to me!"

Rodney turned to John, and despite a look that showed that he'd been experiencing the same, couldn't resist. "Yeah, a memory I'd love to have, but unfortunately never will!"

John ran his fingers into his hair and tugged, hard. Rodney had been getting more aggressive and useless as time wore on. He wondered if that was the effect this place was having on him. "Rodney, I'm going to ask you plain and simple. Do you remember anything that you never experienced?"

Rodney grunted, and wheezed as his lungs protested. "No shit Sherlock, I remember trying to rape Sam. It's not enough for me to be dying, but now every time I close my eyes I see her fighting me… I remember it all… I freaking nailed her on the head with a bottle and…"

Rodney turned away, tears flowing down his cheeks. John realized just how much harder it must be for Rodney, having to experience such a horrible memory that wasn't his. "Rodney… I'm sorry. _Goddamnit_ I hate you and I'm sorry! I don't know how else to say it for the love of…"

Rodney grumbled, and wiped the tears from his cheeks. The pale almost ancient look of his face reminded him of the holographic version he'd seen not too long ago, except that version had hair, despite what John had told Rodney. "Yeah yeah… save the pity. I really don't give a damn anymore. There's your proof of concept Mr. Married to Samantha Carter, you're seeing drunken gravity sex with Sam, and I'm becoming even more cynical than I thought physically possible."

John scoffed, this didn't sound at all like his Rodney. "Come on! Forget about this reality dammit, you and I both know neither of us belongs here, so I'm hoping you've gotten some work done on the jumper."

Rodney waggled his head in mockery, but pulled up the data. "Yeah yeah, I pulled the black box outta the jumper while you were busy making more babies with Sam…"

John froze, god when had he become such an_ impulsive __idiot_? He had no clue whether Sam used any form of protection, and even worse, he had no clue what his own virility was like. Last night had been so reckless that John wondered if maybe he really did bang himself on the head in the Jumper crash.

Rodney continued. "So, what I've found is that that nebula is in the last stages of forming a star, and it's a big one, I'm guessing at least A or more likely B class. For you – the unwashed – that means its…"

John rolled his eyes "Really big and blue, got it."

Rodney turned with an irritated face. "Oh, right, Mensa." He shuddered in distaste and continued; now bringing up the data from the Jumper. "From what I can tell, just about the time we were heading back into the gate, the accretion disk had begun to reach Critical Mass and it's gravitic pull was getting stronger and stronger. Back in our reality, SG-1 had a similar problem when another SG-1 team used a spatial anomaly similar to a black hole to get to our reality and steal our ZPM."

John furrowed his brow. "How the hell did you find that out?"

Rodney shrugged. "Sam told me, our Sam. We were comparing crazy missions and she beat me there. I still blew up more than her so I win."

John sighed, At least a part of his Rodney was still around. "Great, so how do you solve this?"

Rodney grunted, and held the side of his head as if he had a headache, which he most likely did. "To put it simply, we can't. it was a complete and utter fluke we ended up here. Not only is this just a random reality, but I still don't know why only our personalities and memories transferred other than the universe decided to pull a nasty prank on me - which I'm not completely discounting as ever since I arrived in Pegasus, I've become some kind of magnet for horrible catastrophes and unwarranted physical and mental anguish! The jumper may have recorded all the information we need, but in order to replicate it…" Rodney made an indecisive shrug. "I don't think we have the chance here… I was going to send this data to Sam… but that would give us away."

John gulped. He had no clue what was coming. "So what? We just live out the rest of our lives here?"

Rodney scoffed, and angrily muttered "Well, that might be all well and dandy for you mister half-replicator, but you're gonna have to put me in stasis right away if we want any chance of getting back."

John furrowed his brow and thought hard, Rodney was being incredibly pedantic. "Rodney… in English? You just said we can't go back."

Rodney shut the computer off and turned to John. "We wait for our reality to solve the problem for us."

John blinked a few times, curious as to how insane Rodney had become. "Come again?"

Rodney pushed himself up and stabilized with the cane he now always had. "It's reasonable to assume our doubles are in our bodies in our reality. And since they're obviously a lot different from us, it's much more likely they've been caught and Zelenka and the others are working on the problem right now. Since our reality doesn't hate me nearly as much as this one does, which surprisingly has given me a much greater appreciation for what I do have back there in comparison to my evil perverted twin here... they'll work on solving the problem from their end using what I'm guessing is the same data in the jumper. They might even invite Sam back to Atlantis since she has experience with this stuff."

John considered it, it was actually pretty likely seeing as how the John Sheppard of this reality would almost immediately try and… "Oh hell, Rodney. _Woolsey_ - He's one of the bad guys here. I mean if this reality's Sheppard saw him, he' d probably try and tear his face off or something!"

Rodney scoffed, and chuckled once. "That'd be swell, we might even get Sam ba…"

John huffed in amusement, he'd enjoy…

They both looked at each other, thoroughly surprised by their ease of speaking of Woolsey's untimely demise. John cocked his head and rubbed the side of his face. "Ok… this is messed, We need help with this. I'm going to tell Carson."

Rodney's eyes went wide open. "What? Are you serious? He's a doctor and he's _glad_ I'm dying! I can't imagine what he'd do."

John sighed, and put his hand on Rodney's shoulder. "Rodney, I talked to him. Before the… he used to be your friend. He called you his best friend for god's sake. He's more angry at himself than he is at you for not doing enough to help the Rodney here."

Rodney's head came up. "Really? He told you that?"

John nodded. "Yeah, he's… he's pretty close to this reality's Sam and me."

"You mean him, The Sheppard from this universe."

John closed his eyes and shook his head clear. "Yeah, Yeah I uhh… Yeah."

Rodney made a worried sound. "Sheppard, we need to do this now. We're both… we're becoming them Sheppard. I don't know how, but I'm starting to remember things I never did either."

John took a deep breath, and rubbed his face with his palms. "Yeah, alright. I'm gonna talk to Carson, see if we can get you in stasis."

Rodney winced, and held his side, John felt the urge inside to help him, but something kept him back, and this time it felt right.


	4. Guilt

**- Chapter 4 – Guilt -**

"General? Something the matter?"

John walked up to where Carson was working on his tablet in the infirmary and sighed. "You could say that. Is there somewhere we can talk, privately?"

Carson raised an eyebrow, and nodded as he set his tablet down. "Aye, me office should be fine."

John followed as Carson led him to the decently sized office. He looked around the office and couldn't help but feel familiarity. Pictures of Carson and Cadman laughing and enjoying their time together, another of Carson with the Athosian children and a giant plush needle… where he'd gotten it was a complete mystery.

But the one that drew his attention the most, was a picture of Carson, standing beside a bed with a disheveled looking Sam on it. John was on the other side, half his body on the bed… and a newborn baby in Sam's arms as John held her up. A basket on the table next to them sat conspicuously. The flash came to him abruptly, clouding his other senses…

* * *

_"__Is there somewhere we can talk, privately?" John spoke first, feeling he needed to break the ice._

_Carson turned and smiled, seeing the two leaders walk bashfully into the infirmary. "General? Colonel? Something ailing you?"_

_Sam blushed, and looking around whispered. "No, it's umm, it's private."_

_Carson furrowed his brow "Private? You don't mean…?" He raised his eyebrows in shock. "Aye, well, uhh - Perhaps we should step into me office then kiddies."_

_Sam was still blushing, but despite feeling some embarrassment, followed after. John made sure no one was watching too intently and closed the door behind him. He felt like a high school kid getting caught making out in the photography lab. He kept his voice calm. "Carson, I… I mean, we…"_

_Carson shook his hand, and chuckled slightly. "No need General, I've been waiting for this day for awhile."_

_Sam blushed hard and made a really embarrassed sound as she turned into John and gave him a hug, hiding her face as she muttered 'oh god' softly. John sighed and put his arm around her in a tight hug. "Look, It just happened okay? We're…" he looked to Sam. "Working it out. What I want to know is if there are going to be any complications."_

_Carson smiled, but this time without amusement and more out of care. "Aye, I reckon I know what you mean. Like I said, I've been waiting for this and took the liberty of doing some testing."_

_Sam muttered silently, thoroughly humiliated. "You were expecting this?"_

_John kept quiet, unsure of what to feel. Carson's voice showed only care. "Aye lass. I've been keeping an eye on you two for weeks now. Maybe the others don't notice, certainly Rodney doesn't…" He smirked, and rolled his eyes. "… but you two have a certain way about each other… it would have surprised me more if the two of you didn't end up like this."_

_John smacked his forehead, tugged on his hair and quietly murmured. "Just give me the facts Carson… you can laugh at me later."_

_Carson chuckled again, and shrugged in agreement. "Aye lad, just be glad It'll be an inside joke."_

_Sam turned to him, her tone threatening. "It better stay an inside joke… I swear Carson… if anyone finds out…"_

_Carson made a zipper motion across his lips. "Doctor Patient Confidentiality you know? In any case, what I've discovered is that you Sam – the protein marker left from when the Tok'Ra symbiote was in your system left you with a stronger cellular structure and lower permeability factor in your immune system. Basically…"_

_Sam sighed, already knowing from Dr. Frasier's assessment. "I'm not sterile…but I might as well be."_

_Carson sighed in response, but then smiled slyly. "One might think, but when you came I tested against the strongest ancient gene just on a hunch. It's not foolproof, but the ancient gene can adapt itself to be compatible to different situations. The stronger the gene, the more chance Even so, it's still a very minute chance. There's more though, as strange as it sounds, the nanites in your body General are sort of peculiar. When you were infected, I coordinated with Rodney on studying them, and we found out that the nanites in your system are actually incredibly stupid in comparison to other nanites we've discovered. Basically, all they do is repair, and strengthen the cellular walls of your own cells, improve your own immune system by a significant factor, and build more of themselves as needed. Tis all very complicated and such, but basically what I'm trying to say is…"_

_John dropped his jaw in shock; He looked to Sam who was equally surprised, but with the hint of a genuine smile. "We're… we're compatible."_

_"__Aye, and I think you're the only ones who are with each other on this entire base. So… I'll be glad to be discreet if ya want some… protection."_

_Sam and John looked to each other, and realized that this wasn't going to get any easier._

* * *

The memory faded, but John needed to know for certain. "Carson, you weren't sure whether Sam would be able to have a baby with the protein marker in her system… but it turned out the Ancient Gene was able to adapt, and the nanites helped too… Right?"

Carson did a double take, and huffed in surprise and amusement. "Aye Lad, that protein marker makes her cellular structure tougher than regular human DNA and hence, incompatible. But your unique cellular structure had a 1 in 23 chance of successfully adapting, down to 1 in 15 with the nanites." Carson sat, and smiled a wide smile. "It's good to see your memory is coming back. I recall you asking me about it when you and her first…" He suddenly got a bit bashful "Well, you know. Doctor Patient confidentiality."

John was disconcerted by how Carson said it in exactly the same way he remembered it. That was the proof he needed that things were changing in him. If he didn't hurry, he might lose all essence of what he once was to this… this urge building inside him. He only hoped that Carson would be able to give him the last piece of the pizzle.

"Carson, this might sound silly, but I need to know… What is memory?"

Carson was sitting and sipping at a tea he had in a mug on his desk. He furrowed his brow at the question. "Aye well, that's a mighty confusing question you pose there. D'ya mean memory in a literal sense, or metaphorical?"

John shrugged, still unsure of how to put it. "Like… what's it made of? How does memory work in our brains?"

Carson put his finger to his lips and made a 'hmmm' sound. "That's a tougher question than ya might suppose, and honestly speaking we still don't rightly know exactly how the brain works. It just does. One of the more popular and scientific theories is that our brains act much like computers, storing memory onto blank cells for future recall. Amnesia is when your brain can't decode the stored information – sort of like trying to open a file with the wrong program. I can see why you got the sudden curiosity. As far as I can tell, your brain hasn't suffered any damage so I'd say all your memories are still in place."

John had been thinking on the way to the infirmary for a way to tell Carson what happened, but still keep Rodney and him relatively safe. "Doc… I have to confess. There's something really strange going on and I didn't want to alarm anybody more than I already have."

Carson got a look of worry, and sat up straight. "Aye? What's the matter?"

John sighed, and tried to get it out in the easiest way possible. "It's been really strange… when you pulled me out of the Jumper I didn't think I had any memory loss, or what have you… but I didn't recognize a thing because… I remember another Atlantis… and different circumstances."

Carson sat still, contemplating what John was saying. "What are you saying?"

John shrugged. "I don't know anymore… everything was so clear then but… as time is goes by I'm… I'm getting more memories… memories I've had here and not… _there_."

Carson leaned forward, now completely worried. "Your saying you remember another life? Here in Atlantis?"

John had decided it was a good ploy to pretend to be the John Sheppard from here, but have the memories of his own reality. At least…. That's what he thought he came up with. It was just sorta coming out now and it only further confused him. "You could say that. But not a past life or anything… I'm remembering another John Sheppard… one who is very different."

Carson got up, and pulled out a scanner from his bag at the side of the desk. "Hold still, I'm going to run an intensive scan of your brain."

"Uhh… okay." John sat still as Carson ran the medical instrument over his head, he'd never seen this specific one before and furrowed his brow. "Carson…"

Carson shushed him. "Quiet now Lad, gimme a minute to finish this and we'll see what's up."

John stayed still, wondering what this scan would show up, when Carson began making confused noises, he turned to him. "What does tha…"

He didn't get a chance to finish as Carson grabbed his head and straightened it again like a barber. "Hold still you bugger! I won't get an accurate scan otherwise, so don't move till I tell you to."

John didn't want to aggravate Carson further, so he stayed still despite feeling an itch he suddenly felt a great need to scratch. Finally, after almost 2 minutes of scanning Carson turned off the device. "Alright, you can move now."

John instantly raised his arm and scratched, wheezing as the relief set in. Carson chuckled but then furrowed his brow looking at the scan results on the device. John narrowed his eyes. "What? What'd you find?"

Carson sat down, and looked at the results on the tablet. "Well lad… it's strange. When I scanned you right after the crash, your brain scanned normal. But now…"

John resisted yelling. "Oh come on, this whole 'leave me hanging' bit is getting old!"

Carson huffed in amusement. "Ha, well if you want it straight, it looks like your brain is giving off two distinct brainwaves. Sorta the same as when Zelenka and Esposito were in the same body."

John did a double take. "Come again? Zelenka and Esposito? As in Doctors Zelenka and Esposito?"

Carson did a small double take of his own. Then closed his eyes remembering "Aye that's right, you don't remember. During one of our off-world exploring missions, both of them were captured by a Wraith dart we managed to shoot down…"

John finished it for him, extrapolating from his own memories of what happened to Rodney and Cadman. "… and we only had power to restore one of them, but both were inside the same body…"

Carson chuckled, recalling the incident. "Esposito never did talk to Zelenka much after, I think he rather enjoyed being in her body just a wee bit too much. Can't say I blame him but don't tell Cadman that." He focused. "It's good to see your memory is coming back, slowly though it is."

John chuckled for a moment; Cadman had been lucky to be the one in McKay's body and not the other way around. John wondered what kind of effect not having had that experience would have had on Rodney. He lost the grin and grumbled, "This is different though. I'm not hearing voices or being controlled, it's like memories of another John Sheppard are there..."

Carson sighed. "Aye, tis most peculiar. If ye want a metaphor for what I'm seeing, one brainwave is a glass of water, the other is a block of ice. Same stuff, different state. You mix the two, and slowly they begin to coalesce. I think you should go see Sam and see if she can figure out what happened with the Jumper crash, might have been something I missed."

John panicked. It was all the proof he needed that he had to hurry, "So ok, layman's terms; you're saying my memory will come back and the other pattern is fading?"

Carson winced. "Not exactly, they're merging, slowly becoming something that's an amalgamation of the two."

"So it's just a matter of time?"

Carson nodded. "From what I can tell, yes. I haven' a clue how that'd affect you in the long term."

John sighed and kept his voice low, then decided to change the subject. "I think we should put McKay in stasis." Carson stopped everything he was doing. He looked like he wanted to say something but kept to it himself. John still wanted to know though. "What? Come on Carson, this ain't the time to be holding anything back. Spit it out."

Carson smacked his lips, and let a deep breath out. "Well, If you order it General, I'll do it. But I'm curious as to your line of reasoning. Only basis I can see in putting him in stasis is keeping him alive, and we all know where most of the base stands on that."

John swallowed; this wasn't going to be easy. "It's complicated. I've got memories and… well I've just got this feeling that I should keep him around. I can't explain it anymore than that. And if this dual memory thing is happening to me, it's likely happening to him as well."

It was the truth John now realized. He'd intended to lie, to make it seem as if some higher power was calling him to save McKay despite his many sins. But now, even that dark urge within him to just let McKay go in the quickest way possible had changed minds. Both he, _and_ his alternate personality wanted to put McKay in stasis.

Carson considered it and played with his fingers. "Well, I know it won't be the most popular thing you've ordered. I also know well enough now to trust your feelings. I'll get Rodney into stasis right away."

John resisted sighing in relief. Carson would keep his mouth shut, but at least he could be a little more open now. And with McKay in stasis, their window of opportunity just grew. He still would eventually deteriorate even in stasis, but his suffering might be gone. He only hoped his conversation with Sam went just as easily.

* * *

"Hey! Look who came to see us Evie!"

John almost laughed derisively, never in his time knowing Samantha Carter in his own reality would he have ever guessed her to be such a maternal woman. Yet here she was, playing with their child as she worked on a computer console as well as piecing together a Naquadah Generator. "Jeez Sam. Talk about Multi-Tasking."

She snickered, and bounced Janet up and down on her knee. "Yeah well, I haven't been here in awhile, but Carson called a few minutes ago and asked me to take a look at the black box from the Jumper you crashed. He thinks something might have affected you there and that's why your memory was blocked."

John moved forward, and got within her personal space without even thinking about it until it was too late. "Yeah..."

Sam lowered her voice, still playing with Evelyn as she bounced her up and down on her knee. "What is it John? Don't sidestep it, tell me. I can't help you otherwise."

John shook his head, suddenly realizing he'd moved so close. Carson would be quiet, but he didn't want to worry Sam. He found it strange – he felt so protective of her. "Nah nah, it's nothing. Just… I remember, I remember our little conversation with Carson after…"

Sam furrowed her brow. "Our…?" Her eyebrows went up in shock, and then giddy with a little embarrassment and just a touch of red shame to her cheeks. "Oh god, well… yeah. How… how much do you remember?"

John shrugged, and without thinking reached down to pick up Janet. "Enough to know Carson is still laughing at me, and you and me are-" John felt a sudden tug on the side of his head. "What the…?"

Another moment where he had no clue what he was consciously doing. He'd been so lost in trying to understand how he could remember such an awkward moment with Sam and Carson, that he didn't even realize he'd picked up Evelyn and was holding her up high. The baby had reached out and grabbed a tiny fistful of his hair and was tugging on it.

Sam giggled, and made a sweet sound. "Aw, she missed you. Evelyn loves your hair."

John winced slightly and gasped as Evelyn tugged harder. "Ow ow ow, yes I can see that! Ow ow ow…"

Sam laughed openly, and a few seconds later another voice joined in. One John recognized, but only by it's nasallyness. "Oh god, she's got his hair again."

John turned, still holding Evie up near his head and faced the woman. "This hurts you know? And neither of you seem to be in the least bit concerned, I'm mildly offended!"

Both Sam and Lindsay laughed, John felt every one of his actions on impulse, and despite part of him feeling offended over their inaction and laughing, the majority of him knew this wasn't the first time it had happened and actually felt comfortable. Evie finally let go of his hair and settled down on his shoulder. Using her pudgy hands to play with his beard and neck, she babbled happily playing with her dad.

Sam moved in, and looked at John as he stared down at Janet. Lindsay had a small baby boy in a pouch in front of her, and also looked at John. "Wow. It's not often I get to see you like this General. It's nice to see."

John furrowed his brow, and mindlessly began to play with Evey as she babbled incoherently. "Hmm? What do you mean?"

Lindsay bounced the child hanging off her torso like a backpack, and after giving him a little series of pecks, looked to John. "Well sir, you're always so busy. I don't think I've ever seen you down here just to play with Evie."

John sighed, knowing it was true even if he didn't remember. "I, well err…yeah, I guess that's true." He felt his mission tug at his mind. He had to see what Sam had gotten so far, "Well, I hate to do this, but I actually did come down here to do more than…" He looked at Evie again, and felt himself and Sam smile back. She giggled as she played with his hands, but kept pulling on his shirt and beard. His words were pure gut reaction. "Hey there, I'm your daddy."

Sam moved in and put her head on his other shoulder, wrapping her arm around him and looking at them both. "John, you want to hold her for awhile?"

John didn't know what he was doing. The urge in his mind was getting stronger, and he had to actively and consciously think about what he was doing. He turned to Sam, and nodded softly. "Yeah. I'll… I'll hold her for a bit. But uhh, I did actually come here for your help."

Lindsay moved over and sat next to the computer console. "Actually, Sam? Carson called me and asked me to give you a hand with whatever you're supposed to be doing while you do whatever it is he wants you to do for the General… or whatever."

John nearly smacked his forehead. Lindsey was just as nervous as his own reality's version. "Uhh right. Sam?"

He looked to Sam, who was still smiling at him. "Yeah, Carson told me that too." She looked to Lindsay. "I was going to fix this Naquadah Generator for the Gamma site. But if you could do me the favor?"

Lindsay nodded and picked up the tools she'd need. Then waved Sam off. "Go go! Kevin's been up for hours and he'll finally pass out soon and give me a little time to relax and get some work done. Go!"

Sam smiled and gave Lindsey a caring pat on her shoulder. "Thanks Lindsay, Umm John? Could you give me and Lindsay a moment alone? Girl Talk?"

John furrowed his brow, and held Janet closer. "Fine, we'll be over there having fun!" He winced as Evie yet again grabbed a hold of his hair. His comical sarcasm was deflated by his daughter's fascination with his hair, so he rolled his eyes and walked over to the computer where a schematic of Atlantis was displayed. He noticed a flashing button and considered pressing it.

He turned to Sam and Lindsay, who were busy whispering to each other and giggling. _'__Oh great, as if my sex life or lack thereof wasn't enough gossip back…'_ He stopped himself, what was home? He tried to remember… Home was… Atlantis… but not this one… he pushed the thought out of his mind, and decided to be as impulsive as the child he cradled.

Upon pressing the button, a display of what looked like an extra large Jumper with additional sections appeared. John pressed the screen instinctively, again not realizing how he knew what to do.

He examined the ship, dubbed the "_Phoenix_" from the name above. John didn't understand any of the information going past except for a few key systems like engines and weapons, and finally hearing Sam come closer, spoke without even turning. "Sam… what is this?"

Sam walked up, and with no hesitation sat down on his lap and took the baby in her free arm. "_That_ is my other baby." She opened up another file with one hand while cuddling with the other, John seemed to make out a giggling noise behind him, and saw Lindsay about 20 feet away with her fist to her face. _'Hrmm… guess my hearing is pretty strong.'_

Sam continued, pointing out with her finger. "I guess I should start from the beginning. I'm going to assume you haven't seen the logs where you talk about the Travelers?"

John shook his head, not wanting to give away his own experience with Larrin in his reality. "Uhh, no. So how'd we meet them?"

Sam drew in a deep breath, looked like she was about to speak, then sighed heavily. "It's complicated – really complicated. Maybe when we're done here you should go and take a look at the logs…" she clicked the ship again, and a 3 dimensional cross-section appeared. "While Daedalus is our flagship, we've got another 2 ships that use Atlantis as a base. The Orion, and the Traveler Aurora named Spartaneon, Sparta for short."

John raised an eyebrow. "Well, I figure I'm the one who named Orion from that volcano planet. But Sparta? Damn… never woulda guessed that one. That still doesn't answer what this is though."

Sam smiled, and John saw the same smile he'd seen when the Sam of his universe got a good idea. "This… is almost finished. All we need is the supply of Naquadah Daedalus is bringing back now to finish the reactor chamber." She pointed out specific systems and explained. "We designed this ship from the ground up. It uses parts from pretty much every technology tree we have. Any spare parts we had lying around have pretty much found a use in it, A jumper mental interface and cloaking device, F-302 based heavy railguns for dealing with the Wraith and atmospheric ground strikes, and both Asgard and Traveler plasma weapons for heavier engagements."

John smiled. "Ah, that explains Phoenix… So it's a strike craft?"

Sam shrugged a bit. "Sort of. It's more like an assault craft. We built it specifically to move a platoon of troops in and out quickly and provide heavy air support."

John furrowed his brow. "Okay; are we invading anywhere?"

Sam sighed. "No no no… it's not about that. If we had the resources, we'd probably try and build more Daedalus class ships, but it just takes too many resources, and for the same amount of material, we can build 3 of these ships that with shielding, can be just as effective, and a lot more stealthy."

"Hmm… so a mid-sized stealth assault craft. Neat. You came up with the idea?"

Sam scrunched her face, and sighed again. "Well sort of. You asked me to come up with something we could use to stealthily get our people in and out, didn't use drones as its main weapons, and could carry a decent amount of men and materials, with relative safety. Your exact words were 'A Human Al'Kesh."

John mused in half contentment. "Good to know I'm not completely useless."

Sam chuckled as well. "Well, it's not like you don't still go off-world. It's just that…" Sam sighed and rested her head next to his. "Everybody knows you're not going to give up. And since you've got the strongest ATA gene, you feel more at home here on Atlantis. Coordinating everything is just as taxing as running around off-world."

John wrapped his free arm around her and hugged her. "I guess that makes sense." He kept control of himself, and wondered again what exactly led them to the point they were at. Atlantis in space, Larrin and the Travelers joining up, it was all very confusing. "Sam, I'm gonna head back and watch more logs. You gonna be okay with Evie here?" He pushed the happily babbling baby away, and for the moment that no one was holding her, she began to whine.

As soon as Sam pulled her close and bounced her around a bit, she calmed, burying her face in Sam's long hair. "Yeah, there's a playpen in the closet. I'll pull it out and get to work." She smiled at John with genuine care. "I hope you remember everything soon. There's… stuff we need to talk about."

John sighed, and feeling very confused, simply nodded. "I… yeah we'll uhh… we'll see."

Without another word, he left the room and headed into the armored labyrinth of Atlantis. He considered heading back to his quarters, but a sudden alarm warned him that something was amiss. He turned his radio on and heard a cacophony of calls crying over an attack,.

Switching to the command frequency, he called out. "This is Sheppard, Someone tell me what's going on now!"

A few seconds passed, and Colonel Lorne's voice came in the clear. _"General… you might just want to come to the control room."_

John felt his blood begin to rush, the protective being within him suddenly came out to light and he realized. This may not be his Atlantis, but he'd still fight to defend it.

John ran through the halls, the floor wasn't shaking, and the lights were still normal so he assumed that instead of being under attack, something was up outside of Atlantis.

His instinct proved correct, as he quickly entered the gate room to see Colonel Lorne watching the giant LCD screen where information came in. The gate wasn't even active. "Colonel, what's the situation?" Sheppard moved quickly and soon stood next to his XO.

Lorne turned and made a half smile, half frown. "Sir, you sure you're…?"

John didn't let him finish and waved him quiet. "Just tell me who they are, why they're attacking, and what we can do to stop them."

Lorne sighed, and turned back to the screen. "We don't know who they are - and they're attacking our Beta Site. Teyla and Ronon are there right now and I'm guessing it was her who activated the subspace distress call. We've already confirmed we can't dial the gate so it must be active on their end."

John felt relief, but his stomach quickly contracted. "Beta Site, What does…?"

Lorne answered quickly, not bothering to hear the whole sentence. "Trading outpost. There's a large Genii settlement nearby and most of the Travelers who've settled are there. Teyla's in charge of the base."

John rubbed his palms together, anxious over what was happening. "So they're under attack?"

Lorne nodded, and brought up the information. "Yeah, Subspace distress call. Most likely it's a raid but the message says they're well armed for raiders."

"Raiders? As in _stealing_ our stuff?"

Lorne nodded again, getting a little exasperated as he spoke. "Yes, they're what's left of the brotherhood and coalition, Chuck?"

The ever present gate technician raised his head and nodded. "Sir?"

Lorne stepped forward and pointed at the gate. "Set the gate for automatic dialing. As soon as you get a good lock, hold the gate open."

Chuck nodded and got to work. "Yes sir, getting it done."

Sheppard met Lorne's gaze as he turned back to the screen. "So what's the plan? Jumpers? Is Daedalus nearby?"

Lorne smirked. "Jumpers. None of our ships are close enough; We can send reinforcements as soon as we get a good lock." He tapped on the screen and brought up a com link to Sam's lab. "Colonel Carter."

On the screen, Sam turned from her seat and looked. "Colonel Lorne, what's happening?"

Lorne explained the situation quickly and concisely. Sam seemed to understand what he was asking despite not being explicitly told. "So you want to know if _Pheonix_ is ready."

"Basically. Jumper reinforcements are good, but if they have any ships…"

Sam nodded, and rubbed her forehead. "Alright… I'll have to pull a few people off shift, but it should be done soon. I'll call you once it's done…"

She looked across the screen to where John stood, still a little confused over the situation, Without another word, but a look that cut into John, she shut the link off. John looked to Lorne who was now deep in thought. He spoke without thinking. "So Colonel, base under attack, only available reinforcements available are light ground forces, How many do you send?"

Lorne smirked, something that confused John even more than his unbidden words. "Depends on what it is we're defending. So in this case, two jumpers, two squads. One to hold the gate, another to hold the command center while Jumpers lay down air support."

John knew it was right. But… _'Wait…the hell…? Why am I agreeing? This is Teyla and Ronon! We should go in full force…kick the crap out of these raider… but… it makes so much sense… what the hell?'_ He ignored the voice in his head telling him to order a full strike, but decided to compromise. "Colonel, have one of the marine teams meet me in the Jumper Bay."

Lorne raised his brows. "Sir?"

John leaned in, suddenly feeling very angry. "I may not remember why Atlantis is in space, or even what we trade to the Genii, but I'm not going to sit and try and figure out what's going on when I can go and help,"

Lorne fell back a bit, getting into a defensive posture. "Clear sir. I'll have the marines there ASAP."

John suddenly stopped, and after looking at Lorne for a second, turned and headed to the Armory. _'The hell? I'm so… angry! This isn't me dammit, come on, stay focused.'_

It wasn't long before John ended up in the armory, and looking around, he was strangely familiar, yet still a bit confused over the weaponry inside. One of the marines in the room saluted smartly, "Sir!"

John tried to think of what each weapon did, but couldn't exactly understand what each was specifically for. He looked to the marine, a young man whom he didn't recognize. "Soldier, do you know about what happened to me?"

The marine nodded with reluctance. "Yes, sir. Something about memory loss."

John looked away and picked up one of the modified P90s. "Well it's true, so I'm gonna need your help arming up."

The marine raised his eyebrows, and gulping he nodded. "Yes… sir."

* * *

John felt strange in this armor, sitting with a team of marines and waiting in a jumper. Sure it was light, comfortable, but the wires running along his chest and arms made him feel like a science fiction convention attendee for Wormhole Extreme or its spinoff, Elysium City. From what the marine had explained though, the cables were used to bleed energy off from energy weapon attacks. It only served for a few shots. But when facing the wraith, it was completely worth the added cost and resources to make this armor.

The weapon was pretty straight forward though, it was basically a P90 with an added battery pack that powered a plasma projector. Designed using Asgard technology, it fired a small pulse of concentrated high powered plasma for taking out hard targets and Replicators.

From what Lorne had told him, it was likely that in the next few minutes, the gate would dial and they'd move in. So it came as a surprise when Sam entered the Jumper Bay. "John! What are you doing?"

John shifted, and stared back. "I've got to. I just – I need to do this."

Sam moved closer and pulled him to the side away from the marines. "John." She looked like she wanted to argue, to convince him to stay, but after a moment she just sighed. "Be careful John. The nanites might give you an edge but you're not invincible."

John felt a flash of memory, Sam's worried face triggering it.

* * *

_"Lorne! Cover McKay, I'm gonna push ahead!"_

_"Yes Sir! Bates, give me some goddamned covering fire!"_

_Bates moved into position behind the steel girder holding the concrete in place and leaned out. "__Go sir! We'll hold position here!"_

_John nodded and moved ahead. If that bastard O'Neill was here…_

_He didn't get much more chance to think about it, as he suddenly turned the corner and ran into three SGC guards. He reacted instantly, striking out with the butt of his P90E and snapping back as he spun around with his leg. One guard went down with a bloodied face, and the other tripped and fell to the ground._

_The third guard fired, and John felt his armor take the brunt of the shots, but he quickly shrugged it off, and as he turned to the now stunned guard, lowered his weapon to his hip and fired low to avoid the bulletproof vest._

_The burst of P90E fire tore into the guard's thighs drawing cries of pain from the wounded man. John didn't hesitate and put another shot into his head as he fell to the ground, silencing him. The 2nd guard got back up and tackled John from behind, but was surprised when John bucked him off easily. He grabbed the soldier's hair and smashed his head into the wall hard enough to leave a spurt of blood punctuated by the crack of bone fracturing._

_The first guard pulled his sidearm and fired blind, still reeling and blind from the strike to his face. A pair of bullets penetrated John's armor and drew a wince of pain. The nanites quickly got to work sealing off the wound. John was back to normal before he finished putting a final burst into the stunned guard taking him down._

_Under normal circumstances, this was not the kind of fight John got into. The concept of a one man army was foolhardy, but the way the nanites would automatically and without question repair any damage to his body… John decided it was less of a risk for him to move forward instead of ordering others to risk their lives._

_John knew the nanites scared the others, it made him different, and it made him dangerous. But they followed his orders without question, and he gladly moved forward now, feeling the need to prove he was worthy of their loyalty._

_Another fire-team engaged him, this one staying back and trying to suppress him with their projectile weapons. John took cover behind the corner and reloaded the P90. He pulled out one of the three grenades on his Bandoleer, and lobbed it underhanded into the hallway._

_The flashbang hit, and for a moment John was stunned, but he felt a tingling in his eyes and ears, quickly recovering. He jumped out in a crouch, and taking careful aim, put the three enemy soldiers down with a combination of 5.7mm fire, and plasma._

_He took fire as well, feeling the searing heat and pain from each wound. It hurt like hell, but the adrenaline rushing through his veins kept him going as the nanites repaired the damage._

_Finally, he made it. He only had one grenade left, but this was the one he was saving. He'd policed more ammo from the fallen guards, and now with a fully loaded P90E, and a frag grenade in the other hand, he coiled and drove his foot through the door shattering the lock and breaking it down._

_He moved in quickly, getting down to one knee and scanning the room with the iron sight. It was a comfortable room, completely different from any of the other rooms in the SGC. An emperor sized bed was the center of attention though, and John could see someone sitting up, covered up with a blanket. He instinctively aimed, but held his fire. Her voice was final, and completely without emotion. __"Just get it over with. You'll be doing me a favor."_

_He recognized her, she was one of the primary officers of this place, he'd been briefed by her when he first set out a year ago. "__Colonel Carter?"_

_She turned, and keeping the sheets at her neck looked to him with shock. __"Major Sheppard? How did, but… didn't they already send the nuke through?"_

_John held his fire, and pointed the gun away from her. He put the grenade back on his vest and questioned her. __"Nuke? What, where's O'Neill?"_

_Sam cringed; she looked away from John in despair. __"He's not here, he's on the Enterprise."_

_John cursed, and realized exactly what Sam was doing here. The shock of her earlier words finally hit him. __"Wait, oh god you're… He… " __She sniffled and nodded, tears flowing out of her eyes. John stood and felt his stomach tighten and hurt. He couldn't leave her here. __"Come with me. You'll never have to deal with the bastard again."_

_He held his hand out to her, even as the sound of gunfire and explosions came from outside. She panted hard, suddenly coming to grips with the situation. __"You mean it? You'd take me to Atlantis?"_

_John nodded. __"Get dressed, we're blowing this place sky high."_

_Sam drew in a sharp breath. __"I… there's no clothes in here. This is all I've got." __She curled up, trying her best not to cry audibly._

_John felt his rage boiling over. He needed calm, he needed to keep a clear head, so he took a deep breath and then put his weapons down. __"Here; take this." __He took his vest off, and tossed the too large garment to the woman on the bed._

_She sniffled and silently put the vest on. She got up and John averted his gaze. She was bruised and battered, the dark marks on her skin made John swear to do worse to the man who did it. Despite wavering a bit in place though, she seemed determined to follow. __"What's the plan?" __She reached over and pulled the Sig Sauer out of John's thigh holster and with an experienced move, and slight trembling, readied it for action._

_John looked to her and clenched his jaw. __"You ok using that? It's heavy out there." __Sam nodded, and her panting seemed to show the rage that she now let free. Without a word she conveyed her determination to him. John picked up his P90E and opened the door. __"Stay behind me."_

_She nodded and did as she was told; quickly they left the room and moved out. They took a moment to appropriate some clothing for Sam from one of the fallen guards, and just as she reached for his weapon, a burst of fire from across the hall warned them of hostiles._

_John picked her up and used his own body as cover for her. Bullets hit him hard enough to push him back, and he tossed Sam behind the next corner with one hand before falling down with a pained groan._

_Sam recovered, and screamed as she saw Sheppard go down. She pulled the grenade from the vest she wore and priming it, tossed it down the hall. Sam hid behind cover, and covered her ears as the fragmentation grenade detonated in the midst of the fire team, the twisted hot metal of the casing tearing them to rivets in the hard concrete and steel pipe they stood in._

_She waited 2 seconds, then leaned out and aimed. They were still moving, but on the floor stunned and maimed. Without any hesitation, she moved forward and fired the pistol relentlessly. Sam emptied the clip, putting a period to the end of the attacking fire-team._

_Once sure they were dead, she leaned on the side of the hallway, realizing with a heartbreaking point that with Sheppard down, she most likely wasn't going to escape. So when she turned to check on him, and saw him sitting up with a groan, and wipe off his chest where the wounds had completely disappeared, she was obviously shocked. __"Sheppard! But… how did…?"_

_He waved her silent, and still wincing from the past pain took point again. __"Not now… I'll explain later… let's move."_

_She felt fear, and the sudden revival of hope. Perhaps she would escape with her life._

* * *

Sam leaned forward and gave John a hug. "I know it's useless to say it, but don't take stupid risks. I don't want Evie to have to grow up without a dad."

John sighed and returned the hug. The memory of what had happened, even if it was his conuterpart's memory was heartwrenching. He realized that even if this wasn't his family, he still had an obligation to them in this situation. "Yeah, I'll… I'll be careful."

Sam snickered. "Says the man who walks into gunfire." She groaned at her own joke, and kissed him on the cheek. "I know we haven't talked too much about it, but when you get back we'll talk. Love you."

John swallowed, and for the first time since he arrived he decided to tell the truth, even as strange as it sounded coming from his lips. "Love you too."

* * *

"This is General Sheppard to anyone at the beta site. Please respond."

John kept the jumper high in the sky, the columns of smoke that rose from the Beta Site that actually turned out to be a small town warned him that heavy weapons had likely been used. The area around the gate had been hot with bullets, the Jumper taking light fire as it came through. Thankfully none of those heavy weapons had been used against them, A few moments passed and a familiar voice came through. _"John? Is that you?"_

John sighed in relief. Teyla… "Yes! Teyla, we're above you in a cloaked jumper. Who attacked you?" He tried to keep to business, Teyla likely didn't know about his…

Wait… it wasn't memory loss… that was just the cover story. He was from an alternate reality…

John winced and held his head. The thoughts and urges he'd been experiencing were starting to take control. Who was he? _'Dammit… I am… Lieutenant Colonel John Sheppard... Not Brigadier General John Sheppard…I ended up in this place after a jumper crash with my best friend Dr Meredith Rodney McKay… He's my best friend… not the man that tried to rape Samantha… my wife… No…! Samantha Carter is NOT my wife…! we do NOT have a child together…! General O'Neill is my boss…! not my nemesis…! Come on John… hold it together… What'd McKay say? Just wait till our reality sorts it out? Well come on then, Fix this! FIX THIS!'_

Teyla's voice broke his concentration. _"What are you doing here John? Oh nevermind, we need assistance near the gate! Ronon and his squad are pinned down and we can't reach them on the radios, we've gotten word from the Genii that they've come under attack as well."_

John sighed, he wished he could see her face, but knew he had to make due with what he had, he keyed in the other jumper and barked. "Jumper 2, head to the command center and assist Teyla. We're heading to the gate, Copy?"

_"__Copy that General, Stackhouse out."_

John shivered. The real, No… _this_ Stackhouse was just as real as the one from his own universe. So his own Stackhouse was a lot like this one, Ready, willing, and more than capable of following orders. He wished he could have time to examine these people more. See what differences there were from one reality to the next.

He pushed those thoughts out of his mind. Rodney and now Ronon were the biggest things on his mind. He had to save them… both.

* * *

Sheppard was expecting some form of friendly greeting between him and Ronon, but the sudden almost hostile glance Ronon gave him made him question just how much damage the Nanites could repair. "Sheppard! The _hell_ are you doing here?

John asked himself the same question, why had he insisted on coming himself? Lorne could have easily sent trained Marines. The obvious answer was to save Teyla… something he was notorious for in his own reality, But now as he ran through incoming fire, he questioned his logic. John scurried over and took cover next to the tree Ronon was crouched behind, a staccato of automatic weapons fire told him they were in plain view. "Oh you know, I've always gotta be the dashing hero."

Ronon grunted, and leaning out fired off what looked like a grenade launcher. The projectile arced over and a loud bang confirmed John's suspicion. The raiders had cloistered around the gate, holding it as a fallback position and trying to get away now. Ronon started chuckling. "Just like old times huh?"

John shrugged, and leaning out himself fired his P90 at the suspected position they were under attack from. "Wouldn't know, can't remember jack squat."

Ronon didn't seem fazed, and fired another grenade towards the treeline that seemed to spit bullets at them. To their sides, marines set up for a crossfire on the gate. "What, You get whacked in the head or something?"

John flinched and ducked, a high powered bullet dug into the wood where his head had been a moment ago. The splinters washed harmlessly over his cheek "Or something!"

Ronon reloaded his grenade launcher, and screamed into a wrist radio. "Suppressive fire!"

From up in the trees, Ronon's squad fired on the treeline, peppering the entire forest with bullets, plasma, and the occasional concussive grenade. Ronon himself leaned out again and dropped a grenade right by the edge of the gate, the white hot shrapnel not even scratching the ancient ring but wounding the raiders who rushed through. "So you just decided to tag along?"

John raised his rifle, and made out a face thirty feet away in the treeline. Normally he'd be a little confused that he could see so far and so clearly, but instead he just thumbed the safety lock to the plasma rifle, and with a small blue pulse, cleanly decapitated the target. "Pretty much!"

It wasn't long before returning fire slackened, and moving forward, they finally overtook their attackers. They were clothed in regular Pegasus clothing, something that only seemed to confirm Lorne's suspicion of Raiders. But they fought to the last man, leaving no prisoners and no survivors.

The battle was over, and the outpost was secure. Casualties were light but several storehouses had been raided. Ronon was relatively quiet, seemingly accepting of John's strange injury, but not making a big deal. In fact Ronon was having fun ribbing him about it. "So hey, remember when you taught me to snowboard?"

John shrugged, "No Ronon. I already told you, I'm getting bits and pieces back but nothing specific like that."

Ronon chuckled. "Well good, because it never happened!"

John smacked his forehead. If he didn't know better, this Ronon was the same as his own with the constant teasing. All that was missing was the dark brooding the Satedan was famous for. It seemed that without the harsh life of being a runner, the Satedan was actually much more social. "You know, I get the feeling this is how most of our conversations go Chewy."

Ronon chuckled. "You'd be right Han, but it's been awhile since you've been able to take the time to come here."

John closed his eyes and winced hard. His Ronon had _never_ called him Han back in jest, another strange thing about the reality.

They approached the settlement, Teyla could be made out organizing the medical teams and making sure everybody was ok. John muttered softly as they walked closer. "You know… nobody wants to tell me exactly why that is. So I'm gonna ask you a favor. When was the last time I saw you and why has it been so long?"

Ronon shrugged, and patted him on the back. "Too long, and you've been busy preparing for an attack."

John stopped, and looked to Ronon who now turned to face him. "Say what?"

Ronon's tone was nonchalant. "The last of the Wraith have banded together, they're hunting for Atlantis and are culling any worlds they come across. They're on their last leg and are pulling all the stops…"

John clenched his jaw. No wonder everybody seemed on edge because the John Sheppard they knew was acting funny. "… Thank you. I guess I should have expected you to be the one to tell me what the score was."

Ronon shrugged. "Well I owe you, we both do."

Teyla walked up and looked them both up and down. After a moment she moved forward and caught Ronon in a big hug that he returned just as intimately. John was momentarily confused, but then remembered in his logs his counterpart had suspected this would happen. "It's good to see you Teyla…"

Teyla turned from the embrace and looked at John with muted confusion. "What are you doing here? Why are you not preparing?"

Ronon grunted, and kept his voice low. "He had a little accident, can't remember anything."

Teyla raised her eyebrows in surprise. "What? But… that still doesn't answer my question. What are you doing here John?"

John shrugged, and shook his head equally confused. "I really don't know. We got your distress call and Lorne sent reinforcements. I joined in because… well I remember you both… but I thought maybe you could help…"

John caught himself. What was he saying? He didn't need to jog his memory, he needed to hold on long enough for either this universe's Sam to figure out a way to send him back, or for his own universe to fix the problem for him. It startled him just how fast and alluring it was becoming to just blend in, let the new memories and personality take over.

Teyla immediately noticed something was wrong, and took John's hand. "John… you shouldn't be here." She saw the slight pain and confusion in his eyes and smiled "It is good to see you again though. It has been too long."

John sighed, and looked to his two friends. "Feel like bringing me up to speed?"

* * *

The day was almost over, and John had found out a lot of things that happened in this universe differently to his own. Ronon and Teyla had left Atlantis when the Wraith attempted to take the city a little less than 2 years ago, right around the time of the original attempted Wraith attack on Earth. They'd decided to start a new outpost, the Beta Site, in order to establish trade lines with the people of Pegasus without exposing Atlantis. John had been reluctant to send them off, but understood the reasoning behind it.

Most of the Athosians and Satedans they had found scattered about had left with them, and the outposts had flourished by working with the Genii to farm, and generally establish good relations. Ronon and Teyla themselves had grown close, and instead of Kanaan, Teyla had married Ronon after a year on the Outpost. The fact that she didn't have a child was something strange to John. It seemed to be an unspoken reason that after McKay had his breakdown, they didn't feel comfortable on Atlantis anymore.

A year after the outpost, contact with the Travelers was made when Daedalus saved a damaged Traveler generation ship from an attacking Wraith Hive. Larrin had been chosen to be the ambassador to the city, and soon the Travelers joined with the Atlanteans in full union. Those who wanted to settle down joined the Athosians here at the beta site, while the ones who wanted to stay in space joined Atlantis's crew.

With the Traveler's in full alliance, Atlantis had been since converted to mostly Traveler based power generators. With a pair of ZPM's to boot, it was no effort to keep the city shielded and in a remote part of the Galaxy to hide from Wraith, Replicator, and the eventual scout forces of O'Neill held Earth.

At the very least, John had an answer for why Larrin was in command of Daedalus. With Lorne, Sam, and most likely himself taking care of their families, she was the only other person with a high command experience. Major Ford was in charge of the Orion that served as an exploratory mining vessel in deep space to avoid Wraith, or Replicator attack as it had no ZPM to power it's systems.

That was the scariest thing though, the Replicators were still around. Unlike his own reality, the Replicators had never been defeated. While they weren't rampaging across the galaxy, but they were still harassing any and all Atlantean resources.

Things weren't as close with Teyla as he would have liked, she kept her distance throughout the entire inspection of the damage from the attack, staying close to Ronon. He realized that it was to be expected, what with them not being nearly as close as they were in his own reality.

It was amazing to think that this all stemmed from really one act. Jack O'Neill. It was a little disturbing to think that things could get so different, the fate of 2 galaxies hanging in the balance. Not to mention the Altera Galaxy with the Ori in mind, or the Asgard, of whom he still had little idea what happened.

The day was ending, and John decided to head back to Atlantis, The jumpers had been sent back already, and John walked with Teyla and Ronon to the edge of the outpost. He was still a little surprised that these two had become so close, but he'd come to accept it just as he had Teyla's relationship with Kanaan. Though it seemed much too quickly… John began to think that his counterpart had done the same, come to accept them, and now it was easier for him to come to terms.

Ronon and Teyla said their goodbyes, and John walked back to the gate with a pair of Marine guards… his personal escort. They were silent and didn't look like they wanted to talk.

They were just about to reach the gate, John deep in thought over what might happen when he got back, when the gate began to spool up. "Hmm…? Either of you two know if Atlantis is sending more people?"

They both shook their heads, and judging from the quickening pulse in his own chest, he got the feeling things were about to go very wrong.

He didn't have a chance to do anything though, because as soon as the gate opened and stabilized, a large metal ball came out, John had no idea what it was, but he still dove for cover.

The explosion was massive, or at least it felt massive. John went from seeing the gate activating to seeing stars as he groaned from some unseen wounds. A tingling around his whole body told him the nanites were hard at work repairing him, but something else was bothering him.

He was being dragged. By one foot no less, and there were voices.

_"__What about the others…?"_

_"__Leave them… he's the one I want."_

_"__He's a tough son of a bitch, I doubt the others survived it as well as he has."_

_"__We'll see how tough he is without a ship… make sure our man gets out tonight before they realize he's gone."_

_"__Ha yeah, you'd think he'd be smart enough to smell a spy out."_

_"__Quiet now, we've got a lot of work to do."_

John recognized one of the voices. The blood froze in his veins as he realized what was happening. In his own reality, she'd been traded back to the Genii during the Siege in exchange for nuclear weapons. But here… she'd taken over for Kolya…

John finally completely panicked. _'Not again… oh god not again…please god not again.'_


	5. Depression

-**Chapter 5 – Depression **-

John didn't know where he was, or at least that's what he kept telling himself. The dull brown of rusted metal told him exactly where he was… the harsh light shining down on him forcing his gaze to the ground. The cruel tightness of the heavy chains binding him to the hanging pole.

He was barely tall enough to stand with his arms hanging. Just another interrogation tactic… he kept reminding himself that he'd been through this before… and things always got easier the more you did them. When it came to torture though, that wasn't exactly a pleasant thought.

A sinister laugh came from the shadows, and the next thing John knew a lash swiped across his face cutting into his cheek.

The pain was tolerable, but only just. The laugh from the shadows cackled, but then slowly died.

"What is this? How…"

The figure stepped into the light, and John struggled against his bonds to choke the life out of him. "You!"

The man grunted in both shock and pleasure. "Yes… You were so sure you killed me. And in a way… you did."

The heavy set man turned around, and John could hear his knuckles cracking. He braced himself for the hit that slammed into the side of his head, tearing open the skin above his eye and drawing a gasp of pain from John. The nanites quickly repaired the damage, something that shocked the man standing before John.

John felt the need to make his defiance clear. "Come on Kolya… My grandmother can hit me harder than that."

The next hit proved too much, and John felt both his brain jar from the impact, as well as an unbidden memory.

* * *

_John heard a knocking on his door, which was strange given that these doors had bells that one needed only to wave one's hand to activate. In his fugue like half-dream state, he forgot about that and walked his hand straight into the door as he reached for the non-existent knob. He didn't bother asking who it was as he cursed and sucked on his bruised fingers. When he opened the door he was either going to get dressed beyond his boxers, or throw a punch at whoever was disturbing his beauty sleep._

_He waved the door open, and was stopped cold by who he saw standing there. __"Sam? Wha… Jesus what the hell happened to you?"_

_Sam was sniffling, her eyes were red with tears and cheeks puffy. She swallowed as she looked at him and spoke softly.__ "John… I… we need to talk."_

* * *

Back in the interrogation chamber, consciousness crept back to John. Kolya was still looking at him in surprise. "How is it that you can heal so quickly? Tell me now!"

John chuckled, and realized with a suddenly depressed sigh that while the nanites did heal him… in this situation all it did was let them beat on him even more. "Oh I got blessed by a witch doctor the other day. Still hasn't worn off."

Kolya threw a punch to John's gut, his body curled reflexively and he hung from his arms, swinging like a pendulum until he was able to straighten again. His legs were lashed to the ground as well and even as he tried to kick, all he did was manage to momentarily hurt his knees. The pain quickly subsided, but the memory was still there. His stomach ached terribly though.

The Genii soldier was weaker than John remembered… Kolya didn't look as healthy as he'd last seen him, and already the man was breathing heavily. John decided to test the waters. "What's a matter Kolya? Getting tired already? Lost that imposing virility? Maybe I did kill at least a part of you. A _small _part."

Another hit, this time a knee to the groin. John groaned loudly as he lost all the breath in his lungs and his eyes felt like they were straining out of his sockets. He struggled to not cry out loudly. Kolya chuckled and pulled John's chin up. "Perhaps I shall do the same to you then… unless you give me what I ask."

John scoffed, but it came out weak and strained from the prior blow. "This again? Jesus Kolya, not only do you fight dirty but you're still hung up on that? Grow a pair and leave well enough alone. You survived me once, you think you'll live another encounter?"

Kolya sighed, and held his side. "Perhaps your little healing trick will serve you well… or perhaps it will serve us more… As far as my survival… well… you should practice your knife aim a little more." He opened his shirt to expose a nasty looking scar. "A pierced lung, and months recovering was the price I paid for survival – A price I will now deduct from you. I will leave you with one of my old students – I trust you will be a good test subject for her training."

John breathed heavily again, and saw her step into the light holding a quarterstaff. She didn't look happy. "Hey Sora, I was just wondering when you were gonna pop up and say hi."

She smiled evilly, and waiting for Kolya to leave she spun the staff in her hands. "Hello."

John didn't hear anything else, as the heavy wooden staff smacked his head sending him back into unconsciousness.

* * *

_John sighed, and realizing just how much of a train wreck she must have had to come to his quarters at 2 in the morning looking like hell, he pulled her inside. __"Jesus Sam… come on in..."_

_She hesitantly stepped in, and as soon as the door closed she turned and hugged him tightly. John had been in this position before, but not for several months. He wrapped his own arms around her and patted her shoulder. __"Alright. come on now; just let it out. I'm here Sam."_

_She cried hard into his chest, his skin growing slick with her tears. John led her over to the bed and sat down, pulling her along with her. She curled up and kept a hold on him, just like all the nights before. This was different though, as she finally broke the intense contact and looked him in the eyes. __"John… I'm so sorry I've been such a… "_

_John shushed her, and shook his head. __"What else could I do? Jesus Sam… I tell everyone but it goes double for you. I'm here till the end and I'm not gonna abandon anyone."_

_Sam laid her head down on his chest again, nuzzling against his bare skin. John usually slept in his boxers, but in the time he and Sam shared a room he'd taken to wearing a shirt to sleep to avoid these situations. Seems that surprise had given him the proverbial kick in the ass for not being diligent._

* * *

"Seems you're a lot tougher than the last time we met. Good. I'll get to enjoy this more."

John had just opened his eyes, then regretted it as he saw the staff bounce off his chest that made a sickening crack sound. He could almost feel his ribcage cave in, but then immediately begin to repair and protect his internal organs. He clenched his jaw in agony, the pain was unbelievable as he coughed and spit up blood. But within a minute his ribcage had been fully repaired, and the pain just a searing memory in his brain. "Well this is getting old quick… Are you even gonna bother asking me anything?"

"I've been studying your people Sheppard. Ever since you killed my father I've been wanting to figure out exactly how many bones of yours I could break before getting my revenge."

Another thwack, and John's arm cried out in anguish from the impossible angle it hung in. He tried his best not to scream, but still let a loud groan slip his mouth.

This was not the same as before. The pain was astonishing. The fact that these damn Nanites just repaired him for the next barrage was a fact that made John realize just how much of a curse it was. His arm reverted back to its normal position soon with a loud crack, and he felt the beads of sweat trickling down his neck, impossibly itchy. "Looks like you'll have a good long time to find out. Unless you _fuck up_ as usual."

A hit to his stomach, and the contents of his stomach suddenly were in his throat. He held it for a second, and taking careful aim, spewed his lunch in her direction. She jumped back too late, getting coated in the bile mess of half digested Loden Bird sandwich.

Sora didn't say a word, and drove the end of the staff right into Sheppard's forehead knocking the clarity from his vision.

* * *

_She spoke softly, but with a calmer voice. __"I haven't told you everything yet John, there's a lot I tried to bury – a lot I tried to forget."_

_John nodded and held her close.__ "Yeah."_

_Sam relaxed, and let John support her completely. __"I thought I was okay John. I thought once I left him behind I'd… well it would take time, but I thought I'd be okay." __She looked up into his eyes. __"…and I was okay, at least for awhile."_

_John didn't let her go, and instead rubbed her shoulder softly. It had been awhile since he and his second in command had had a heart to heart. He didn't think she ever really talked to anyone else about this… baggage. __"What changed?"_

_Sam gulped again – almost afraid to say it. __"I moved out of this room… and I tried to live a normal life."_

_John half scoffed. What was she saying? __"There's no crime in that Sam. Kinda hard to lead a normal life though when you're floating on a city that's god knows how many years old and still a mystery to us."_

_Sam kept sobbing softly, and squeezed him hard. __"I miss you John, I know I see you every day but…"_

* * *

John came back to the land of the living, wondering what was real. Was he with Sam talking about their relationship or lack there of? Or was Sora the crazy Genii chick still beating the crap out of him?

A stabbing pain in his leg told him it was the latter, and he cried out in surprise. His leg twitched, and Sora watched in fascination as the knife began to jiggle, and soon popped out harmlessly as the Nanites pushed the obstruction out of the way of their programmed parameters of rebuilding.

"Impressive. I sliced a big artery there and you still healed… I wonder how much healing you can do before you run out?"

John wondered that himself, and also whether parts of him would grow back if… he pushed that thought out of his mind, no sense giving them ideas. "Not a clue. Like I said, witch doctor. Something about Louisiana and garlic chicken."

Sora grunted again. John had no clue how long she'd been at this as not only had he been knocked out several times, but she'd also changed clothes. Given the beads of sweat running down her chin, and the surprising tattered state of his clothing, he figured awhile was a good guess. "Keep laughing. We're just getting started."

John braced himself, and felt another massive thump against his chest, this one very direct and clearly shattered one of his ribs. He wheezed suddenly, as he felt his lung being pierced causing him to cough in pain. The agony was getting to be too much, and John didn't know how long he'd last under the strain. "Oh come on! I'm the fucking god of war here! You gotta hit me like you mean it! Come on! Really throw your back into it!"

Why was he taunting her? She just beat him harder. Was that what he wanted? To show them he wasn't going to break? That no matter what they did to him it didn't matter? As he felt his foot shatter from the hammer like strike, and quickly begin to repair, he wondered exactly how stupid, and how far Sora and Kolya would go amidst his repressed cries of anguish.

Another knock to his head, this time the back of his skull, and he was out.

* * *

_"John, I have to tell you; because it's killing me to be the only one who really knows."_

_They were laying back on the bed now, she curled up against him. Comfortable as she whispered. __"You don't have to jump in with both feet Sam. I've waited this long."_

_Sam shook her head, and took a deep breath in. __"You know what the worst part is? He used to be a good man…"_

_John reacted, tensing his body. __"It's... hard to imagine."_

_"I don't blame you for not believing me John – you had to know him." __She sighed heavily and squeezed John, a signal to him to hold her tighter. __"He was a good man; a family man. He had a son, Charlie. He was such a sweet kid."_

_John kept his breathing under control. Getting angry wouldn't help anything here. __"Most kids are."_

_"Not like this, I've seen old videos of him and…" __She sobbed softly, taking a moment to word it. __"…they both seemed so happy, He wasn't anything like the man he is now."_

_"Kinda hard to picture that."_

_Sam bit her lower lip, and finally decided to tell him. __"It was at first… when he came back from Abydos he was… he was happy. We couldn't exactly tell why I mean, his family had died in a car accident a few months previous and here he was with a captured alien ship smiling. It was so strange."_

_"I guess the SGC just figured he felt useful again. What was he, like 50 back then?"_

_Sam snickered darkly __"47 actually…"_

* * *

John awoke again, wondered how many times this had happened, and muttered loudly. "Hey, where's the masseuse? I was expecting a back massa…"

His quip was interrupted as he felt the staff shatter against his back. And for a few brief seconds, he felt the horror of no longer feeling anything below his hip. Through the torturous agony of splintered wood in his back, he tried to move his legs.

The most sickening sense of relief came as the splinters were pushed out, and his feeling returned to his legs. John couldn't take much more of this, but he hoped Sora was even more tired from giving such a profound asskicking. "Sora… just a question. You seeing anyone? Cuz you know I have an open relationship and I love it rough so…"

He felt the blackjack hit the bottom of his neck, and the sudden shock sent him back into la-la land.

* * *

_"What do you want from me Sam? Really."_

_Sam sighed softly, and pressed her body against him under the covers. __"Maybe I'm tired of standing in a crowd and being alone. Everybody looks at me and goes 'there she is, O'Neill's bitch.'" __She tightened her grip on John, obviously feeling anger. __"At the SGC, they all figured I was all for it. Almost none of them would listen if I said otherwise… Those that did usually got sent to war. And here? Everybody treats me like a Ming vase."_

_John made a questioning noise with his throat. __"Hmm? A Ming vase?"_

_Sam smacked her lips and breathed out slowly.__ "Beautiful to look at, too fragile to touch." __She laughed as she scoffed. __"You know McKay's been trying to… well I know what he thinks. He thinks he's helping me by taking me out, bringing me lunch, treating me like I'm some lost little kid he's turning into a princess." __She sniffled once, more out of anger than sadness. __"He's terrified of me, like he's going to break me if he kisses me. I'm not a kid and I'm not a princess. I'm tired of it… I… I want someone who isn't afraid. Someone who isn't looking at me and seeing what they think I am."_

_John understood what she meant. And realized what she was doing here. __"Sam… I… I don't know what to say."_

_She reached up and pulled herself closer to his head. __"I don't want you to say anything. I, I want you to kiss me… __really__ kiss me."_

_John looked back at her. She was barely 6 inches away from him. He could smell the bead of sweat trickling down her temple. John didn't know what to do anymore… This woman had thoroughly and completely broken through all his defenses and now he was leaning forward to kiss her._

* * *

John awoke yet again, _'this is getting old…'_ and looked around at his surroundings. He wasn't hanging anymore, so that was a good thing. He was lying on a bed, with the same heavy shackles holding him down_. __'guess they're not taking any chances.'_

He tried to look around for a bit, and then finally decided to take a chance. "Hello? Anyone out there? I'm kinda thirsty!"

A few moments passed, and he could hear someone breathing nearby. He tried to turn his head far enough, but he couldn't. "Hey! I hear you! I can hear you breathing!"

The breathing stopped for a moment. And after a few seconds started again. An all too familiar voice rang out, the strange tremor and flux of the voice gave John true fear. "So I see Kolya has found a new pet… perhaps I shall feed soon."

John pulled on his chains harder. Todd had fed on him before, but he wasn't in any mood to try it again. When they didn't break he simply gave up and sighed. "No escape plan? Figures. So when's breakfast coming?"

* * *

Round 2… that's what John was thinking as they dragged him out of his cell about two hours after they'd tossed him in. Todd had been reluctant to speak so John passed the time trying to think of how he was going to kill Kolya this time. Shooting him in his own reality now felt like an act of kindness.

His shackles were cruelly tightened, but he found it comical that when they tried to tighten the one around his feet too much, the nanites pushed back hard enough to snap the steel brace. His laughter only brought more pain, as he quickly was struck in the head with the butt of the Genii Guard's rifle to prevent any escape attempt.

He'd been dazed from the hit, and before he knew it he was back in the same room as before, this time being hung from his feet and suspended in the air. He felt the blood rush to his head, but quickly dissipate. He couldn't help but feel as if his body was under a flight suit.

Sora was in the room, sitting down at a table and watching him intently. John – never one to be afraid to talk to the ladies – muttered even as his hands were lashed down to the floor. "You know… if you wanted a punching bag, you could have just asked… This whole hanging me like meat is pretty old to be honest.

Sora didn't laugh, instead she seemed intently fascinated with the specimen in front of her. "Funny."

John could barely see, but he clearly felt a sudden deep stabbing pain in his side. The drips of blood that ran down his face got into his eyes and he grimaced as he tried to blink it away. A moment later, the ninja star like device clattered to the ground, and the nanites in John's body quickly healed the wound and drew what blood was on his skin back into his body. The little pool beneath him though stayed still.

It was hard to breath, his ankles felt like they were going to pop out of their sockets, but even with his 180 pound frame they remained solid, yet agonizingly stressed.

John had never been so glad to have had the experience with Teer in the Time Dilation field. To be able to dissociate one's physical and mental being was pretty much the only thing that kept him from screaming as Sora now got up and carved into his chest with a razor, the nanites healing as she cut. He focused on mental clarity, and he repeated a mantra _'__Pain is just weakness leaving the body… the mind is separate…'_

He drew in a sharp breath as he felt a burning sensation not far from his groin, a hot poker on his inner thigh threatened to break his mental state. Sora didn't seem fazed at all, simply curious to see his reaction. "You're a lot tougher than I would have thought…"

John panted as Sora finally pulled the poker away, and saw Sora kneel to be face to face with him. "Oh yeah… I've had a lot of practice you know?"

Sora's foot smacked against his face, and John felt his nose crack from the hit. The taste and smell of his own blood had him coughing and choking until the nanites repaired it. "Hmm… How can you keep taking this? I've killed you 20 times and you're still frustrating me…"

He couldn't resist snickering at the upside-down way she looked. "What can I say? I love aggravating the people that try and kill me."

Sora growled softly, stuffed a dirty cotton rag into his mouth, and turned back to the table. "You're a surprise Sheppard. No one's ever lasted this long." She turned back and what looked like a vial was in her hands. "But we've never had reason to use our full potential."

She tossed the vial at him, and the weak glass shattered against his stomach. The acid inside instantly began to burn his skin and John bucked back and forth as the scorching agony made him convulse. It was unlike any pain he'd ever had and if the rag hadn't been in his mouth he would have howled in agony. The nanites in his veins pushed the acid away from his skin and created a small physical shield to keep his cells from deteriorating.

The acid seemed to bead on his skin, and instead of burning through him even more, it flowed off and mixed with his the pool of blood on the ground. It sizzled and created a nauseatingly disgusting gas he was forced to breath.

John tried to push the rag out of his mouth, but it was stuffed so deeply it wasn't happening. He struggled to somehow come loose, but seeing Sora now grab another wooden staff, he braced himself for what was coming.

His thigh was her first target and his muscles flexed in response to the strike, John grimaced and his body quivered as she struck him again and again. John forced himself to think of something else, anything else but the unbelievably excruciating pain Sora was putting him through breaking bone after bone..

He tried to remember his home, Atlantis. It was getting harder and harder to recall exactly what it was like...

The pain suddenly subsided, and Sora's heavy panting brought him back to reality. His vision was blurry, probably from a strike to the head he hadn't noticed while disassociating. But the rest of his body ached and he felt his bones pop back into place.

A sense of anguish washed over him, but not physical. He missed his family… the people who two days ago he didn't know existed.

Sam. He'd never thought of her as anything more than a friend and comrade. Their daughter. _His_ daughter… god this reality was so different. The memories that slowly came back to him made him lament the thought that he might not see them ever again.

_'__No…. no you can't think like this John… you got out of this before… you'll get out of this again.'_

"Alright… I think maybe your tongue might have loosened up a bit." Sora leaned over and pulled out the rag. He gasped and groaned from the weakened state his body was in. "Tell me… how do you heal so quickly?"

John panted and looked up at Sora. "Alright alright, there was no witch doctor…" he tried to look defeated, and recalled something. "I was on this experimental rocket you see, along with Ronon, Teyla and McKay. We got hit by a cosmic ray burst and we formed our new team, the Fantastic Four!" Sora furrowed her brow, obviously getting annoyed. "I'm Mr. Fantastic, McKay is the human torch, Teyla's the invisible woman, and Ronon's The Thing!"

He closed his eyes as he saw Sora's boot coil up and drive into his forehead. He welcomed the unconsciousness and the sweet bliss of not feeling his wounds.

* * *

_This was not what he was expecting to happen._

_"Hey…"_

_Her face seemed like soft silk on his chest, drawing a line across his pecs and the valley between them. Her hands rubbed the tired muscles in his shoulders and arms, almost healing the soreness away._

_This was not what he was expecting to happen._

_"Hey…"_

_John looked down at her… the soft light of the moons outside reflected on her eyes, and John couldn't help but smile at the almost fairy tale setting he was in right now. __"Yeah?"_

_Sam rubbed her legs along his calves and thighs, he let a small moan out as her belly rubbed against his hip bones. She leaned up and kissed him along his neck, almost as if she didn't want to risk having him leave. __"John, you're not… you don't regret this do you?"_

_John sighed, and ran his fingers through Sam's hair.__ "What? No, god no."_

_Sam mused softly, still rubbing her naked body against his.__ "Well, you're kinda quiet."_

_She sniffled again, and squeezed him tighter. John grunted softly, and kept his voice low.__ "Nah, it's just = god Sam, this is the last thing I expected."_

_He brought her face closer and kissed the side of her head. She mused softly and cuddled harder.__ "I, I wasn't expecting it either."_

_John chuckled softly.__ "Don't take this the wrong way, but you coulda fooled me."_

_Sam giggled softly and started to rub his bare legs again.__ "Mmm, I haven't felt this way in a long time."_

_"Felt what way?"_

_Sam breathed in with a sad gasp. __"Like a woman." __she was quiet a moment, John softly stroking her hair. __"You know, I haven't been touched like this in a long time."_

_John sighed emphatically, this was getting a little more melodramatic than he was used to. __"Oh god, Saaam."_

_Sam shushed him and kissed him softly.__ "John, you need to know. This isn't, I'm not trying to pay you back or anything. It' s just, I've been feeling so alone."_

_John stroked his fingers through her hair, enjoying the soft feel of her body against his.__ "Well Sam, I figured you needed some space. I think we all thought that."_

_Sam shook her head and kneaded the stiff muscles of his back.__ "You know, that first week, I almost killed myself." __She waited a few moments to let the words sink in. __"I felt so alone John. I'd never see Earth again, or if I did I'd have to shoot my way in. My family is most likely dead or in prison, Cam's gone renegade, T'ealc and Daniel went with him and started a rebellion. Jack… I tried John. I tried to leave with Daniel; he stopped me. I'm the only one Jack really stopped. He hurt me so bad John. All I ever saw of him was when he wanted… something."_

_John didn't ask. The answer was obvious. He simply drew her in closer and planted a soft kiss along her brow, she started sobbing softly and squeezed him even harder.__ "Shh…"_

_She kept crying softly, but nuzzled against him.__ "I know, that's why I'm here; You're always here for me, and you aren't afraid."_

_John didn't fully understand.__ "Afraid? What do you mean?"_

_Sam stopped crying and pushed away from him. She laid back on the pillow and sighed dejectedly.__ "You're not afraid to touch me. You don't fawn over me like I'm some… specimen." __She sat up on the bed now, breathing heavily. John didn't say anything as it was obvious she needed to get this off her chest. __"You remember last week? My sore neck?"_

_John grumbled softly. He __**had**__ enjoyed giving her a neck rub in his office late that night. Why was she bringing it up now?__ "Uhh, yeah. You made it pretty obvious you wanted me to."_

_Sam nodded and sniffled again.__ "Same thing happened with Rodney. I hurt my shoulder moving a generator and, god I made it so obvious. I could see it in his eyes, he wanted to, but he just called Carson down and…"_

_John finally understood. Rodney was afraid of offending her because of what had happened to her back on Earth. John on the other hand was very comfortable around Sam, probably from the countless nights they'd spent in the same room. Even after the Wraith DNA mishap, they were still comfortable being close.__ "He just wants you to be okay. We all do. You know he, well…"_

_Sam nodded, and reached over to find her clothes. __"I know. But I don't want to be treated like a china doll." __She sighed as she took hold of her shirt. __"I should go, maybe this was a bad idea."_

_John reached out and took her arm as she tried to get up. He wrapped his arms around her waist and kissed her behind her ear.__ "Don't go…this wasn't a bad idea… just… unexpected."_

_Sam sighed in contentment, and leaned back into his muscled arms. __"It was good wasn't it?"_

* * *

John groaned in pain, or at least he would have if that damned rag wasn't back in his mouth. He wasn't upside down anymore so he took that as a good sign, but he didn't feel any better.

Soreness was a blessing compared to what he felt now. Sora had put him through the paces of his endurance and the Lieutenant Colonel in him hated to admit it, but memories of the Brigadier General were the only thing keeping him going. It gave him a level of disassociation that amazed even him.

It was so strange, the memories that surfaced were probably some of the most emotional in the man's life… his life… but not really his. John couldn't tell exactly anymore.

Sora never even asked him any more questions. All he remembered was the pain, the constant and excruciating pain she put him through.

* * *

John wasn't in any sort of a good mood. Sora had spent the last three hours from what Alterna-Todd had told him, beating the crap out of him and laughing as his body repaired itself.

The pain was unbelievable. Every time they shattered one of his bones, cut him with a knife, or on one occasion poured acid on him, he felt every single nano-second of pain until the nanites managed to repair and stabilize the injury.

He was the perfect torture subject, and the only thing keeping him from breaking was the memories that were jarred loose every time they struck him.

It had seemed so strange, one moment cuddled in bed with Sam, the next wondering why his back felt like he'd been stabbed, and then realizing it had been.

It was unceasingly frustrating to Kolya and Sora that he only spat back witty, and to them, incomprehensible comebacks. His explanation for how he healed went from being blessed by a witch-doctor, to being an ascended being of godlike powers, being one of the Fantastic Four, to finally having eaten smiling mushrooms in a land known as Super Mario World.

Each had met with more and more injuries, finally ending with getting stabbed with a red hot poker. That was the worst. Burns always bothered the hell out of him, but to feel his spleen set alight was a sensation he would never wish on anyone… except maybe Kolya.

Now he was back in his cell, with what passed for food in this hellhole. He brought the stale bread to his lips and forced it into his gullet. _'__Atlantis is coming, they'll know right away I've been captured. Sam'll check out the DHD and figure out where I am, I am not going to get fed on again, I am not going to get fed on again…_'

"Yes… eat… soon I shall drain the life from your veins and savor your strength."

John couldn't help but chuckle. "So I guess the two of us working together to escape this place isn't exactly an option for you?"

"With your strength in my veins, I shall need no help… least of all from a destroyer of worlds."

John sighed, somehow he knew the words fit, yet he still wanted to know what his counterpart had done. "Help me out here would ya? What exactly have I done to become Oppenheimer?"

A growl of anger, then a moment of silence, it was unlikely the Wraith would know of Humanity's father of the atomic bomb, but it still amused John that Todd had used such a similar phrase. Todd kept his voice low, almost respectful. "You would ask me to list your crimes John Sheppard?"

John sat up, which was significantly harder than it sounded as he was covered in heavy chains. "Believe it or not, I got wanged in the head and don't remember jack squat about anything I've done in the past 4 or 5 years. So yeah… humor me."

Todd stood there, across from his cell in another, the trademark scar on his face larger than the one in John's own reality. "What is this? A game? You know what you have done to my people Sheppard. I almost respect the callousness of it."

John scoffed. "Respect from a wraith? Damn, now I gotta know what I did."

Todd glared lasciviously at him; John could almost imagine him smacking his lips. "You are serious? You do not remember?"

John tried to scratch an itch that needed to be scratched, but couldn't reach from his heavy bonds. So he silently endured the tingling and shook his head. "Not a damn thing, this whole "Destroyer of Worlds" thing sounds pretty cool though, tell me about that."

Todd growled, and sat down as he spoke. "Your people arrived 5 years ago, and through means I still do not know, infiltrated the city of Atlantis."

John nodded "Yeah yeah… I know all this; get to the part where you respect me."

Todd scoffed, and spit in his direction. "I will thoroughly enjoy your life Sheppard. I have no doubt I shall be regarded a hero for ending it."

John forgot about trying to talk to him, and laid back down his pathetic meal. "Been there, done that, shoulda killed you when I had the chance" He muttered the last part, unsure of whether Todd would hear him.

"Killed me? We have never met… I have spent the last 2 years trapped in this godforsaken cell with Kolya feeding me his prisoners…" Todd growled angrily now, frustrated at his capture. "They all gave him the information he sought… as will you."

John shook his head, how could he give information he didn't even remember? "Good luck with that… amnesia… remember?"

Todd laughed, and leaned on his cell glaring at John lasciviously. "Very well… I shall humor you. I respect your ruthlessness in combat. I have no doubt you've reduced the majority of your enemies in my time here to little more than radioactive vapor, or mindless minions."

John chuckled as he heard Todd's words. "Wow, I'm a real asshole aren't I?"

Todd growled. "Some would call you that. I would call you a more than worthy adversary."

John leaned over and looked to him. "Well, let's just say I kinda sorta maybe respect you too. For reasons you'll never know, and some which I honestly forget."

Todd shook his head in bemused confusion. "Your people are strange Sheppard, but I do find your strength appetizing."

John furrowed his brow and looked at his cellmate. "That's… disturbing to hear."

* * *

"Bring him, the other as well!"

John woke up from his dreamless sleep. He was actually kinda glad as the sudden flashes of memory he had while being beaten were incredibly disconcerting.

He really was becoming the John Sheppard of this universe, not just in body, but in mind as well. It was getting harder and harder to remember more than just feelings and bits and pieces of his former reality. Sort of a complete reversal of what he had originally felt.

John was an angry man, and despite Todd only telling him a little he'd done, the flashes of memory had told him even more.

* * *

_"Sir, Wraith forces have completely overrun the city. I can see processions of people being filed towards the gate." __Stackhouse's voice was calm, but one could hear the frustration behind it._

_John watched as Lorne acted. The commander of Daedalus sighed and opened the channel. __"That explains no Hive… they're taking them to a Wraith planet."_

_"I'd assume that sir, we've been hittin' their hives pretty hard any chance we get so maybe they're trying new tactics."_

_Lorne sighed, and looked to his second in command, a young Lieutenant named Bromwell. __"Lieutenant, how many people are being taken to the gate?"_

_A few quick taps on the console, and Bromwell brought up the image from their sensors. __"One moment… computer estimates around 2 to 3 thousand prisoners being escorted, and another ten thousand still on the run."_

_Lorne kept his cool, and asked all the right questions, __"Do the Wraith have any infrastructure, or heavy weapons to speak of?"_

_"No sir. But we're looking at half-battalion strength forces here. Mostly drones as well as their commanders."_

_Lorne clicked his tongue. __"We can't let them take those people; I'm ordering our men to engage."_

_John stepped forward and kept his voice strong. __"Belay that. Order our men back to their jumpers and set Railguns to atmospheric fire."_

_Lorne turned and looked at John. __"Sir?"_

_John remained unflinching. __"That's almost five hundred Wraith Colonel. We've got what? 2 squads down there? 20 men versus 500 isn't a winnable fight. Maybe if we had some weapons emplacements or time to plan. But we don't."_

_Lorne clenched his jaw, but knew it was the truth. __"Even if we only hit the Wraith, the blasts will probably kill a bunch of civilians as well."_

_John softened his expression for a moment then looked to Lorne with an iron gaze. __"The cost outweighs the price we'd have to pay if we don't."_

_Lorne didn't look that happy with the order. But realizing that sometimes in war, one must do terrible things to win, turned his radio on. __"Captain Stackhouse… get your men back to your jumpers and retreat to a safe distance."_

_"Sir?"_

_"We're going to fire on the Wraith from up here, use your Jumpers to fall back and cover the retreating civilians."_

_John looked at the screen and mentally sighed. From the look of the formation the Wraith were using, and his own assessment of how panicked the prisoners would get when 10 millimeter shells traveling at relativistic speeds slammed down on their captors, he made an educated guess on casualties._

_It had gotten too easy to make this guess, and John had a sneaking suspicion it was going to be fairly accurate. He recalled an ancient Earth saying… the road to hell is paved with good intentions._

* * *

John felt the cruel shackles on his neck tighten. He could barely breathe as the steel collar was attached to a long hollow tube and he was led like a feral animal. To his side, Todd walked with only a stockade like device on his hands impeding him from feeding.

He knew what was coming; the ransom demand, the allowing Todd to feed on him. But he didn't know how he knew anymore. His memory had become a discombobulated mess in his head and he didn't know what to believe.

Was it him who had ordered Daedalus to fire that day? Or was it the other? Did it really make a difference anymore?

The lights were low, and he could hear the Rogue Genii soldiers grumbling and laughing at his situation. He didn't even have a shirt anymore, and the hot bunker made his skin slick and dirty with sweat. He couldn't help but think of gladiators of old, forced to face their death in an arena. He almost wished it was actually that, as he'd rather fight Todd for his freedom, than whatever Kolya had planned for him now.

It wasn't long before he entered a large room, and Todd was held a few feet away. Kolya stood to the side with a large primitive looking screen and bulky camera. It looked like a reverse engineered version of the style the MALP's used.

Kolya tossed a cup of water onto Sheppard, and laughed as he spit the salty fluid out. That was cold – salt water on a prisoner. "Well Sheppard. It appears Sora has treated you well thus far. Are you ready to tell me what I wish to know?"

John felt his collar jerk to the side and he struggled slightly against it. His breathing had gone shallow, but somehow in his mind he knew that nanites were compensating, drawing oxygen in through his skin even as his throat was compressed. "Urrgh… remind me… was that before or after she tried to make out with me?"

A cruel lash struck his back, and he groaned in pain. The torn skin quickly healed, and another pair of lashes were administered before Kolya held his hand up. "Enough, he will obviously not listen to pain of his own… so perhaps pain of another will loosen his tongue."

John worried they had captured another Atlantean. It was perfectly possible. In his mind he considered, what would he do? Would he let Kolya torture another man or women in front of him and stay silent, or would he take the risk and give him what he wanted to know? He had no clue who the hell he was anymore and it scared the hell out of him.

Kolya would never keep his word, so John felt entirely safe in his decision to spit more wit at his captor. "You think that tactic'll work? I'm unbreakable Kolya. Just like Bruce mother fucking Willis!"

He felt a searing pain, he couldn't see it but he could feel the red hot brand push against his back and imprint onto his skin. The worst part was the distinct smell of his own flesh cooking. He couldn't hold it in anymore and screamed in agony as they held it in place.

Finally the pain was too much, and his mind sent him into unconsciousness.

* * *

_John ran through the hive, cursing himself for allowing that Genii Soldier to try and rescue the cocooned victim. He'd brought hell down on top of them and John wasn't eager to become lunch. Damnit he wanted to help these people too, and so did Teyla, but John's primary concern was the mission._

_So when the younger Genii, Alwin, had tried to pull the disoriented man from the wall and the alarm went off. John hurriedly ordered Teyla and Cowen back to the Jumper while he held off the Wraith._

_Alwin had just gotten the cocooned man out, when a Wraith stunner nailed him in the back of the head sending him sprawling to the ground. John didn't even bother trying to pull the man away as he could already see the Wraith in the corridor, and instead threw a grenade to slow them down._

_Even with his P90E, taking on a column of Wraith was suicidal. John was pretty much alone now and with the Life signs detector telling him there were at least a dozen wraith only a few corridors behind him, He had to move fast._

_He was almost to the Jumper, the Nuke had been set, and he was just about to congratulate himself on surviving another suicide mission when he bumped into the older Genii, Tyrus._

_"Major! Where is Alwin!"_

_"He's lunch! __Move goddamnit!__"_

_"What! Why didn't you help him?"_

_"Get in the jumper! The Wraith are on my fucking heels!"_

_Tyrus wouldn't listen, and instead raised his gun to Sheppard. __"No! You killed him!"_

_John couldn't wait, the Wraith were so close… __"Tyrus get out of the fucking way! Stay if you want but I'm the only one who can fly that ship. If you don't move out of my way we're ALL going to die!"_

_Tyrus didn't move, and instead hesitated as he held the gun towards John. __"You monster, you left him to die!"_

_"Tyrus, last chance, Move or I WILL shoot."_

_Tyrus didn't listen, and instead aimed the gun towards Sheppard's head._

_John reacted, it wasn't often men got this close with guns pointed at him. The nuke was set to go off in 4 minutes anyway so even if Tyrus had a chance to go back for Alwin, it was pointless. He had to get his team and Cowen out. Nothing else matter._

_So he raised the P90E, and with no hesitation fired. Tyrus went down instantly and fired a single shot into the ceiling, dead from the bullets penetrating his heart._

_John cursed himself again, and ran towards the Jumper. The first mission with the Genii and they'd taken two casualties… this did not bode well for their diplomatic relations. Weir was gonna castrate him._

* * *

John awoke again, still kneeling but being held up by his restraints. His back no longer burned but he knew it was because the nanites had healed him. The scorching agony had finally broken his threshold of endurance, and he looked with weary eyes up at the screen.

The Atlantis Command Staff… just like he'd seen them before… somewhere. Lorne stood in Weir's place, defacto leader of the expedition if John fell. Sam sat next to him, noticeably bothered by what she saw. Ronon and Teyla were there as well, murderous glares directed at Kolya… McKay was the only one missing, but John knew he wouldn't be there.

Kolya was speaking; evidently John had been passed out for the beginning of this. "…ability has proven quite detrimental to his sanity. I would not be surprised if he does not regain any form of civility after we're finished."

Lorne growled back, obviously furious. "You should know better than others not to mess with us Kolya. Even your own government doesn't want anything to do with you."

Kolya raised his hand. "Ah yes, my former Protégé. How is Ladon? I'm sure he is much better than General Sheppard."

At that, a heavy staff came down on Sheppard's chest, shattering into pieces and yet again crushing his ribcage. He let out a loud groan of agony, complimented by wheezing coughs as the nanites reformed his body.

Sam turned away, obviously not wanting to show weakness on the screen. Ronon growled intensely, as did Teyla. Lorne simply kept his face calm and quietly spoke. "You can't stay hidden forever Kolya. And when we find you. I'm going to make sure your death is _very slow_, and _very painful._"

Kolya chuckled. "It is good to see we agree in tactics then! For you see, I have something that perhaps will change your minds as to how invincible your leader is."

The pair of guards restraining Todd undid the shackles on his stockade, and kept their guns trained on him. A collar with a long metal staff was attached as well, and he was guided to where Sheppard was held on his knees. Lorne visibly became alarmed. "Kolya you cold blooded mother…"

Kolya shook his head. "No Colonel. I am not the cold blooded one here. Our Wraith friend here will judge just how cold the blood of your leader is." John chuckled, and Kolya turned to look at him. "See now? He laughs in the face of death! Were he not such a monster I would perhaps respect him."

John looked up to Kolya and laughed even harder. "I'm gonna enjoy killing you again."

John felt something tugging at him. A small sense of some feeling telling him that no… he doesn't enjoy killing his enemies. But it was soft, the same feelings he'd been having before were muted, muffled.

Todd growled, and his saliva dripped down John's forehead. "This is almost enough to make up for my imprisonment here…"

John growled back, and spit at Todd. "Go ahead, do your worst. Hold back the enzyme." His voice rose to a scream. "Do it! I know you want to! Make me feel every last bit!"

Todd was visible shaken. But his hand still restrained he looked to Kolya who simply muttered. "Have your fill my friend."

John closed his eyes and braced for it. He felt Todd's hand slam hard against his chest, the penetrators digging into his skin. Todd did as he was told, none of the enzyme flowed into his chest.

It was excruciating, John didn't even bother trying to fight it and howled in anguish. He could only imagine what those on Atlantis watching were thinking. It seemed to last forever, but the pain suddenly died down. Todd had pulled away in shock.

John looked down at his chest that was already healing, near delirious from the pain, and began to laugh maniacally. He hurt like hell, but not from a feeding. "Hahaha! Sorry! Buffet's closed!"

Todd growled furiously again, and dug his hand even deeper with a second blow. John screamed as the pain moved along his limbs from his chest, and again passed out from the sheer agony as he convulsed.

* * *

_"Wh… where am I?"_

_John smiled, and began the ruse. __"Whoa there, take it easy. You've been through quite a shock."_

_The man shook his head as he woke up, and suddenly felt dizzy. The two men beside him held him down and tried to reassure him. __"What, what…"_

_Carson shushed him and made it look as if he were busy injecting something into his IV. __"Calm down lad, you're only waking up just now and I'd rather not have you push yourself."_

_The man breathed heavily, still in shock. __"But, I don't… I don't remember anything."_

_Carson and John exchanged looks, and both sighed. __"We know. It's a long story, but we're here to help you."_

_"But but, I don't even know my name."_

_John looked to Carson who nodded softly. John looked down at him and gave him a smile. __"Your name is Michael; Michael Kenmore."_

* * *

John came back to some sense of consciousness; the taste of bloody sweat caressed his lips, almost intoxicating. He saw that Todd had been taken away but the pain in his chest still remained. It was quickly subsiding and he could make out Kolya arguing with Lorne. "…immune to the Wraith… No matter. In the end there are ways of punishing him that are just as painful."

He wasn't ready for it, but seeing his chest rip open from the sudden shotgun blast was the last thing he ever wanted to see. His brain shut off again, protecting him from the agonizing pain.

* * *

_"So Lieutenant, what do you think of your new posting?"_

_Michael nodded and shrugged about a bit, his almost southern accent and sincere smile were slightly disconcerting when John thought about where he'd come from. __"Well sir, it's comfy. Watching over a mine, making sure all the miners are healthy and taken care of."_

_John nodded and sighed in relief. __"I'm glad, most of those people didn't have any other hope, and by working with us we're giving them their independence back."_

_Michael chuckled a bit. __"Yes Sir, they're all happy with the work they're doing since it's not that hard with the transporter tools we have. Nothing like what I thought mining would be."_

_John chuckled. __"Yeah, sorry 'bout keeping that from you when I sent you, Carson says I have a strange sense of humor but I hope you ain't holding it against me."_

_Michael laughed heartily now. __"You kiddin' sir? It's great! I've been reading the logs you sent me and well, after hearing about how I was part of the team that raided the SGC last year, I can totally appreciate such a steady job."_

_John held his finger up. __"Tut tut tut… Just cuz it's steady doesn't mean we don't need it. Or that I'm not capable of reassigning you."_

_Michael instantly straightened. __"Uhh Sorry sir, what I meant to say was…"_

_John cracked and started laughing. __"Oh man, I wish I had a camera. Your face was priceless…"_

_Michael sighed in relief and chuckled himself. __"Yes sir, I… I bet."_

* * *

John woke up again, this time on his side, the collar was off, but the heavy shackles holding him to the ground made escape impossible. He opened his eyes and saw on the screen that only Lorne was left, staring with a vicious glare to Kolya.

Kolya on the other hand was making his demands. "…ask you for Atlantis… Instead, I will only ask that you replace your lap dog Ladon Radim with my other Protégé and give the Genii their pride back."

Sora stepped out, she didn't look so smug as she did before. Maybe John's resistance was finally getting to her. Lorne scoffed and shook his head. "Glad to know who I should put on the hit list."

Kolya growled and again looked to Sheppard. "Then your leader will die. He will experience pain like nothing I had ever imagined possible, but he will die and you will forever deal with the knowledge that you could have saved him."

John saw it this time, the hot brand in the shape of an infinity symbol. He got to brace himself this time and felt it press against his chest. Again he screamed, but the pain was getting more tolerable from the unyielding torture the imposed on him, he managed to hold his scream momentarily and looking at Kolya as he pressed the brand against him, spat with the last of his saliva. "Come on! More! Break me if you fucking can!"

Kolya raised his eyebrows in surprise, and backhanded Sheppard cruelly with his sidearm. John felt his teeth begin to come loose, but quickly tighten as the nanites repaired him. The brand was off now, and his chest reformed. Even his hair was regenerated.

Sora was off at the side watching impressed, though as soon as Kolya turned back she went back to her perpetual scowl. Kolya growled softly and muttered to John. "Today will be the last day of your life if you do not order Lorne to acquiesce to my demands. I will have you crushed in a hydraulic press till you are nothing more than paste."

John closed his eyes and winced, would the nanites be able to fix _that__?_ He doubted it, though in a way he almost welcomed the death that was coming. So he took a few deep last breaths, and looked up at Lorne, his voice finally cracking with sorrow. "Evan…"

Lorne softened his features, and looked at his commanding officer. "Yes, John?"

John bit his lip, and decided on exactly his wording. His jaw quivered at the very thought of what he was about to say. "Take care of Sam and Evie for me would ya? Field promotion to General."

Lorne took a deep breath and visibly held back his fury. "Yes sir, Thank you Sir."

Kolya's growl became a scream, and he shot John with his side arm in the chest over and over until the clip was empty.

John felt most, if not all his internal organs punctured. He couldn't breath, he couldn't feel his pulse, and he thought that maybe the nanites weren't going to heal him fast enough this time. He drifted into blackness and the last thing he saw was Kolya shut the link off.

* * *

_"General, sir… I'm not too comfortable thinking we should be doing this sort of thing."_

_John waved Carson's gentle voiced concern away. __"You're the one who made the virus."_

_**"Retro-**__virus." __Carson corrected him as he looked at Michael heading back through the gate. __"And I don't regret it… but to give them false memories? And to put them to work?"_

_John sighed, not his most popular decision, but with a whole hive worth of humanized Wraith, what else was he supposed to do? __"Carson, you're the closest thing I have to a conscious other than Sam, and she agrees with me on this. All the Wraith we use the retro-virus on have to go somewhere, and we can't keep them here on Atlantis."_

_Carson shrugged indecisively and kept his voice unsure.. __"Aye, but…"_

_John interrupted. __"Yes yes; is it ethical to tell them they're mine workers and get them to work for us? Probably not. But is it anymore ethical to just kill them? It's not like they have anything else."_

_Carson sighed heavily as Michael vanished into the event horizon. __"I understand, I guess I just never really thought about anything beyond turning them into humans."_

_John took Carson's shoulder and gave him a supportive squeeze. __"I know Doc, that's what I'm here for."_


	6. Anger

-**Chapter 6 – Anger **-

John awoke to the sensation of being dragged, For some reason, he felt lighter. He realized he was lighter as most of the heavy shackles had been taken off. His hands were bound behind him in a steel cuff, and his neck was back inside the collar with the long tube to control him. He looked around silently, and saw several labcoats floating about beside him.

They were going to experiment on him. That was clear. Kolya had lied about killing him so quickly. John felt despair, and prayed that whatever Lorne was planning took place soon.

He was weaker than usual, maybe the Nanites were running out of juice, or maybe he just hadn't eaten anything in awhile. The stale bread and unknown meat they'd given him earlier wasn't very appetizing, and he wondered what exactly it was they'd given him.

The door in front of him opened, and a theater of medicine came into view. Wraith blood plastered the walls, with splotches of red as well. Kolya had obviously been busy, and John was the latest subject to this house of horrors.

The pushed him along cruelly, hitting him with something akin to bamboo sticks. It stung like hell, but after the pain of the past two days, was completely disassociated. He fought back where he could, but soon they had him on the table and were transferring the shackles to the table.

None of them said anything, all completely desensitized to such a macabre thing to do. They attached his feet first, using a savagely tight iron cuff to hold him down. They strapped his chest down with leather belts, tying him down very firmly.

And that's when John saw his opening. They uncuffed his hands, and 2 men each tried to force them into the cuffs. He fought as hard as he could, using the reserves of stamina and strength to fight them off. He grabbed the nearest Labcoat and held him by the throat, only squeezing hard enough to hold him and not kill him.

The 4 guards jumped on him and tried to pry his hand away, and while they were distracted with that, his other hand yanked the sidearm from one of the guards on top of him.

He bucked them off with a flail of his arms, all 4 guards were momentarily stunned, John didn't hesitate, and pulled the trigger efficiently as he put the four guards down quickly from point blank shots to their heads. His reaction time was through the roof – probably amped by the nanites in some strange way. The small heavy rounds tore their heads clean off splattering the area with blood and brain matter. He leaned his head up, and seeing the 3 labcoats now running away in terror, he shot 2 in the back putting them down, and the head labcoat with the plastic mask in the leg disabling him.

John breathed hard, there was no doubt someone had heard them, and now he had to hurry. The keys for his bonds were most likely well out of his reach, so he leaned forward, bit down on one of the loose leather straps, and aimed the gun at the bonds at his feet.

The bullet broke the lock, and lodged itself into his ankle. John groaned loudly as the pain shot up his leg that shook in agony. After a few moments, the pain subsided and he took aim for the other one.

A loud bang, a scream of anguish from the bullet, and John was free. He unstrapped the leather belt around his chest and heard movement outside.

He rolled off the gurney flipping it with him as the 3 guards rushed in firing. He could feel the bullets pinging off the metal bed he used as cover, and he leaned out instinctively and fired with the new gun he pulled from the dead Genii on the floor beside him.

The large pole hanging off his neck made the fight harder, but even as he choked he managed to empty the clip of the Genii weapon into the attacking guards without taking any fire himself, instead getting covered in the blood of the Genii who'd rush him. He tried to breath but couldn't, the pole had lodged itself in some grating and he couldn't move anymore.

John calmed down; panicking wasn't going to get him anywhere. So taking a moment to think, his mind suddenly became clear, his actions smooth and eloquent, not blurred and chaotic as they'd been for days. He knew what he had to do, and despite a small feeling of… something… he couldn't tell exactly what it was, he could actively ignore it.

So John positioned himself, and taking a few deep breaths, raised his arms that still had the original cuffs dangling off them with a few links of chain on each, and drove them both from opposite directions into the hollow tube. His felt the bones in his arm fracture from the hard hit, but the tube snapped and waiting a few moments for his arms to repair. John realized he had to make his escape now.

John remembered now, he remembered what happened and it made his blood boil.

* * *

_John had been talking with Lorne about the latest project he and Sam had proposed, The Phoenix Stealth Assault Craft. It was a good idea and they both agreed to take it to Larrin and her engineers when the call for security came over to Sam's Lab._

_John looked to Lorne who instantly nodded already being privy to their relationship. It was late in the day and neither knew what had happened. John had already begun to run when he tapped his earpiece. __"This is General Sheppard, Someone tell me what's going on!"_

_A few seconds passed, and as John ran through the hallways of Atlantis he could already feel the lead weight in his stomach grow. Carson's voice came in in a slow wavering tone. __"Sir… I think you should come down here, right now."_

_John went into a flat out run, people moved out of his way as he rushed through, slowly noticing more and more security personnel arriving to the floor where Sam's lab was._

_It was almost surreal as he stepped in. most the doodads and devices Sam worked on were strewn about, papers littered the floor and John could distinctively smell the copper tinge of blood as well as Athosian wine. His fears and worries pulsed his adrenaline as he desperately looked around for Sam._

_He saw her on the floor, looking catatonic while Carson stitched a gash along the side of her head. He moved closer but Major Ford stopped him in a bear hug before he could get to the point where she could see him. __"Sir, sir!"_

_John was panting; the rage that someone might have attacked Sam overrode all, if any inhibitions he might have. __"Who…__**who**__?"_

_Major Ford pulled him away, anyone else other than Carson and he would have thrown them aside in rage. Aiden's voice was furious as well. __"General, General… Sheppard!" __At the mention of his name, John finally paid attention. __"Sir, It was McKay. He was wasted. I came here to help Carter move a generator, he was…"_

_John didn't need to hear more. He knew exactly what McKay had done. Sam's torn clothes said all he needed to hear. __"Where?" __Ford didn't reply immediately. __"You deaf soldier? Where the hell is he?" John barked._

_Ford groaned as John took his collar and lifted him off the ground and seemingly threatened to throw him over a table. Carson turned around and saw the scuffle, but knew better than to get involved just yet. Ford grunted out his answer. __"He's in the brig, sir!"_

_John put Ford down and stormed out of the room._

_The walk to the brig was a long one, and John couldn't get there fast enough. He had to know what had come over his friend, what could have possibly made him do what he saw in that Lab._

_Damnit, he knew McKay liked her, probably even loved her. But to go this far, this __**vile**__, John silently prayed that some entity had taken over the stocky Canadian so at least somehow it wouldn't be completely his fault, not entirely his obsession._

_When he reached the brig, a pair of marines were outside the forcefield cell, guarding the sick man inside._

_He was beat up pretty badly; lying in the fetal position in the center of the hold. Rodney groaned at the multitude of bruises over his body. He'd been sick and the contents of his stomach lay in front of him. It smelled like sickly wine. John looked to the Warrant Officer and stared right through him. __"Open it."_

_The officer nodded, and quickly keyed in the pad next to the cell. John stepped in and the field came back up. John took a full minute to examine the man beneath him… Sick, badly injured, and barely breathing. Finally John turned and looked at the two guards. __"You. Leave. You, get out and wait for me."_

_The lower ranked soldier nodded and quickly left. He'd heard enough reports of how ruthless John Sheppard was in combat, so he could only imagine what was about the happen. The warrant officer sighed and nodded, taking position outside the room but still in earshot._

_John spoke sternly and gave McKay a gentle kick to the chest. __"Get up."_

_McKay only groaned, and coughed from his bruised gut. __"Uggghh…"_

_John crouched and got close. __"I said, __**get up.**__"_

_McKay rolled over slightly and seeing John began to sob._

_John didn't care, and as he got up he used his foot to finish rolling the Canadian onto his back. __"You know, I overestimated you. I really did think you were okay after Arcturus."_

_McKay coughed and slurred his words. __"I's was never ukay."_

_John resisted kicking him, and instead just tried to stay calm. __"You fooled me."_

_McKay coughed again and looked to John with a mix of hate and jealously. __"So easy for you. everything just plops into yer lap. Nanites… General… Sam." __He said the last word with an odd mixture of lust and disgust._

_John snapped, and drove his foot into McKay's chest. Not hard enough to break anything, but more than sufficient to hurt the man. McKay groaned loudly as he turned over again, recoiled from hitting the force field, and ended up on his stomach facing away from John. He spit blood as he coughed dirtying the floor. __"Urrgh! *cough cough*"_

_"Alright McKay." John snarled. "Since you seem to think it's __so__**easy**__ for me to just abandon everything I knew… have my own leaders try and kill me just because of my genes." John paused a moment and murmured. "…have my mind and body violated by a bunch of fucking machines." He shook off the memories and continued. "And then to top it off, I have to deal with a damaged woman who I saved from a megalomaniac all while taking charge of an entire city. Yeah, I certainly have it better than you."_

_McKay finally sat up, the stench of Athosian wine drifted from his clothes and bloodied mouth. __"I lost everything, but I had nothing… I never had anything to start with…"_

_John sat down across from him, knowing that if he remained standing he'd probably kill McKay right now. __"You had us. We were all here for you. Jesus, isn't Katie Brown fawning over you ever chance she gets? I told you to go for it! How the __fuck__ can you possibly explain what you did?"_

_McKay scoffed, and held his side from the pain he was feeling. Every word was racked with sobs.__ "You're so naïve, you think I was ok? I __**hate**__ this place! Everywhere I look there's someone who does what I do better, I'm nothing here."_

_John clenched his fists, he wouldn't be able to repress his rage much longer.__ "And what? You think you're useless? You're my fucking chief of science! Everybody knows you're a whole different level of genius!"_

_McKay snorted in derision, his voice slowly losing the slur. __"Then why do you always have Sam double check my stuff? Why did Arcturus happen? Why is she the one you always listen to! And why didn't you tell me you two were…!"_

_McKay began to cry again, this time shoving his face into his knees as he wept. John sighed softly and spoke just a tad gentler as he realized what it was McKay was furious about. __"Don't kid yourself, She's my XO. I don't have the time or understanding to check it. You know well as I do I listen to you." His voice grew more dangerous. "As far as me and her…That's really none of your goddamned business. When I brought her back I never intended for that to happen."_

_McKay spat acid. __"But it still did! You knew what I felt about her and you still did it you bastard! You're worse than Kirk! I should be with her! She needs me!"_

_John breathed heavily, was this somehow in some way his fault? __"You're telling me this is all about her? You tried to…you, because you love her?"_

_McKay shook his head, and tugged on his hair. __"Yes… no… I don't know anymore! Goddamn you Sheppard! You're everything I'm not! You don't even have to fucking try and it all comes to you! I, I…"_

_John tugged on his own hair. Rodney had always been a friend and he'd forgotten how fragile he could really be. But that didn't excuse his actions. __"So that gives you the right to try and take what you want from her?"_

_McKay winced hard, and his words came out confused. __"I, I didn't. It wasn't, no… did I? Its…"_

_John finally couldn't take it anymore and walked over to him. He loomed over and grabbed his collar. __"I'm not going to kill you. In fact I'll do you a favor… I'm going give you a reminder of what you've done so for the rest of your pathetic little life you'll know how weak you were. You're going to continue as a scientist for us and you'll damn well respect my authority and charity. But if she wants to kill you, I won't stop her."_

_McKay grimaced in horror, and wept uncontrollably as John picked him up, and slowly drew him closer to the edge of the forcefield. Without a word and completely ignoring any of the scientist's cries and pleas for mercy, he drove his already bloodied face into the energy field._

_The scientist screamed from the burning sensation, his skin slowly sizzling as John forced him to stay there. John didn't feel regret, he didn't feel remorse over what he was doing. He'd learned to live without those things, it was the only way to survive in this harsh galaxy._

_He held him there for almost a minute, finally letting him drop to the floor unceremoniously. McKay's face was almost unrecognizable, the charred skin steaming from the impact. He curled up into a ball and wept uncontrollably while crying in agony. John called out to the warrant officer to open the cell, and soon was out in the hallway._

_The walk back to Sam's lab was shorter – almost too short. He wanted time to think, time to figure out exactly what he was going to do about this situation. McKay might have finally lost it, but he was still a genius, and as such, useful._

_He made it to the lab, and Sam was still on the floor in shock. Carson looked to John and seeing the blood on his uniform, became nervous. __"Sir? Is… are you alright?"_

_"Doctor. Go to the brig and ensure Dr McKay will survive his injuries."_

_"Sir!"_

_"Do it Doctor. We'll talk later."_

_"But…"_

_**"Carson!"**_

_The Scottish man knew better than to press the issue with John, and decided to err on the side of caution. Taking his kit, he walked out the lab and motioned for the guards to follow him to leave Sam and John alone. John slid down the wall and sat next to Sam, a few inches separating them._

_He didn't say anything, and they remained motionless for almost two minutes until Sam finally spoke with a soft tone. __"I'm going to kill him."_

_John nodded softly, and sighed. __"I won't stop you."_

_Sam sniffled, and held her head where a bruise had formed around the cut. __"That his blood?"_

_"Yep."_

_"Did he tell you why?"_

_"… Yep."_

_Sam leaned forward slightly and winced as the headache continued. __"He loves me, and he tried to…" __She cracked slightly, and her sniffles were muffled by her attempt to stop. __"… he tried to…"_

_John put his arms around her and brought her close to him. She let her control go and began to sob into his shoulder, hugging him like it was a buoy in a storm. John ran his palms along her back and smoothed out her ruffled hair as they rocked back and forth. He didn't say anything, and again he was just there for her._

_"I'm gonna kill him John and you can't stop me."_

_"Sam… I don't want you to."_

_Sam instantly drew back, suddenly looking at him with contempt. __"What? How can you say that?"_

_John leaned back against the wall and contemplated everything that had happened since he entered this city. The choices he had to make, the blood on his hands, and as he looked at the torn woman in front of him, he knew he couldn't bear to see her like that. __"Sam… killing in combat is one thing. Killing in cold blood is another altogether."_

_Sam was panting, but it wasn't out of fear, her anger was threatening to boil over. __"What? What do you mean?"_

_"Sam, look at me." __John sighed heavily. He'd come to grips with who he was. But it still sucked to have to be 'that' guy. __"Look at me! Would you say I'm a good man?"_

_Sam nodded without question.__ "Where are you going with this?"_

_John winced. He'd hoped Sam would see the truth but in her blind rage she wasn't coherent. __"Sam, I've killed men, women and children in the name of survival. I'm __not__ a good man. I'm the man that gets things done no matter the price and everybody is completely fucking terrified of me. I'm beyond redemption and I know it… You and Carson are the only ones I'd really say are my friends. Everyone else respects… but they're more scared of me and what I'm capable of doing than anything else."_

_Sam sniffled and shook her head. __"No… no everybody respects you because you kept them all alive… and what does that have to do with… this?"_

_John looked to Sam, and his features softened as he gazed into her eyes. __"You once said everybody treated you like a ming vase… beautiful to look at, too fragile to touch. I don't think you're fragile, but I don't want you to become hard – cold like me."_

_Sam stopped shivering, and looked to John intently. __"You're not gonna let me kill him…"_

_John shook his head. __"I can't stop you, but I can tell you that you'll never be the same. When you have to look in a man's eyes and know that you'll live whether you pull the trigger or not… it changes you." __He took Sam's hands and brought them to his lips. __"I don't want that to happen to you."_

* * *

John tried to pry the collar off his neck, but groaned in pain as it was securely fastened. He heard more alarms outside and knew they were coming for him.

He policed the weapons from the fallen guards, and walked over to the wounded Labcoat who still tried to crawl to the door, leaving a bloody smear in his wake. "Hey!" He put his foot on the labcoat's injured leg and aimed the gun to his head. "You've got five seconds to tell me where the exit is, or they'll have to use a bucket to clean you up."

He pulled back the hammer on the primitive pistol, and put his finger on the trigger. The labcoat winced hard and quivered in fear. "Out the hallway. keep going straight and to the right. Please, please don't-"

John pulled the trigger. The wall behind the labcoat was caked in a mixture of blood and brain matter. No sense leaving witnesses.

John moved with a purpose, he was armed with the pistols the guards had worn and now he moved through the corridors with stealth. A pair of guards appeared near the end of the hallway and John ducked into the shadow of a corner. They hadn't spotted him but were heading his way.

John waited until the passed by and without hesitation put a bullet into each of their skulls above the neck. They never even had a chance to scream but more guards had doubtless heard the commotion.

He pulled more ammo off them and kept moving, following as the Labcoat had said, straight and to the right. He passed by the room where they'd spent hours testing his healing ability, his blood still coated the floor where he stood. He bathed in the rage of the moment, and kept moving.

Another guard was waiting on the other side of the torture room, and as John opened the door he quickly began to yell and tried to draw his sidearm. John lunged forward, and despite taking a bullet to the thigh, managed to subdue his opponent by bashing his head into the wall hard enough to crack his skull open. The guard fell to the ground convulsing and emptying his stomach onto the floor. John limped for a few feet until the nanites were able to push the bullet out and repair the wound.

It was autopilot, No control over his actions beyond escape. John let his body do the thinking as he engaged another patrol of guards. He kept to cover, using his superior training to overwhelm the relatively militia style training of the Rogue Genii. Bullet after bullet flew through the corridors. Soldier after soldier fell before John's rampage.

John was the only survivor, repeatedly taking fire, brushing off the pain as his body grew accustomed to it. It no longer fazed him, he was almost more machine than man at this point. He crippled, then finished off the Genii one by one, using stolen firearms, his boots, and even the chains still attached to his wrists as weapons.

He kept pushing forward, and eventually reached an elevator. A younger Genii soldier tried to attack him with something like a bat but John quickly overpowered him. He tore the bat like device out of his hands and smashed the man's kneecap, breaking the sensitive spot and crippling the Genii soldier. John got in behind him and wrapped his arm around the man's neck.

John knew snapping a man's neck wasn't easy. The human body has muscle that will resist the movement. John pulled back and brought the man to the floor as well, using gravity, torsion, and physics on his side. Two parts of the same object heading in the opposite directions, in this case the man's head and his body, created enough force to herniate the spinal disks in the man's neck, and cut the all important spinal cord inside. The cartilage tearing gave that ever so satisfying 'snap' sound John was after.

John took a moment to shove the dead Genii out of the way of the door of the elevator, and pressed the up button.

At least he'd thought it was up.

When the elevator began to head deeper, John cursed and began to hit the panel trying to get it to go in reverse, but as soon as he managed to figure it out and get the elevator heading up, it suddenly stopped and the lights went off. "Crap."

The grating in front had a wide slit for the floor beneath, and John quickly opened the door and squeezed his way through it despite the scraping.

The hallway in front of him was dark, and he now had no clue where to go. So he moved forward and kept a watchful sense of what was around him, He might be tough, but that didn't mean he couldn't be captured again.

Some movement from up ahead told him someone was coming, and he hid behind a column, waiting for them to close. It took longer than he expected, but seeing the mechanic armed with a wrench in front of him almost made him chuckle. He jumped out, grabbed the man, and quickly subdued him with a chokehold using the chains on his wrists to get him under control.

The man resisted, but hearing the gun click next to his head, he quickly stopped. John kept his voice low and threatening. "You're only alive because you're useful, the more useful you are, the more chance you have of living. Understood?"

The mechanic nodded, and made soft gurgling noises as he tried to speak. John softened his grip and kept the gun on his head. "Alright, alright please don't kill me."

John pulled him off to the side but didn't let go. "Answer and I'll only knock you out. Where is my stuff, and how do I get back to the surface?"

The man nodded again, and pointed off down the hallway. "That way… I'll open the doors for you… there's a lockdown."

John growled sarcastically. "Oh great, I run into the one disloyal soldier in this place, isn't that convenient?"

The man grunted as John squeezed, he spoke fast. "Listen! I'm not one of Kolya's men! I'm a spy from Ladon Radim! He sent me here to-"

John squeezed even harder, pulling the man to the ground and digging the barrel of the gun into his head. "Maybe I was hasty, I think I will kill you."

"Wait wait wait! Let me prove it!" The man begged.

John was about to pull the trigger when a little urge hit him. It said not to pull the trigger, and to give the man a chance. It was so strange, John never took chances like that. "Alright, make your case. _Fast_."

The man nodded and began to speak fast. "Alright… Evelyn."

John froze, and while still holding him in position whispered as menacingly as he could. "Who?"

The man gasped at his movements, and spat his information out fast. "Gods, Evelyn! Your daughter! Her name is Evelyn! When she was born Ladon Radim sent her..."

As the man spoke, the memory flashed before John's eyes.

* * *

_"General Sheppard, Major Ford here."_

_John was content, Sam lay on his chest relaxing. It had been an enduring event, and poor Sam was exhausted. Even so, she still held the newly born baby girl in her arms, who surprisingly was quite docile despite the trauma of birth. __"Yes Major; If Atlantis isn't under threat of being blown up, this really isn't the best time."_

_Ford laughed on the other end, he knew damn well what had happened in the infirmary. Lorne had experienced the same not 2 months prior with his own child. __"Ha ha ha, we're lucky today, sir. It's only the Genii. Ladon Radim would like to have a word with you."_

_John rolled his eyes, Ladon gave him hero worship and it could get annoying. It was Sam who punctuated their feelings. __"Does he realize what agony I've been in? If this is something simple tell him I'm going to pull his tongue out with my bare hands."_

_John chuckled, and tut tut'ed Sam. __"Shhh, you really want our baby to learn to talk like that?"_

_"Coming from mister curse every other word…"_

_John laughed again softly, and listened to Ford's explanation. __"Actually sir, that's exactly why he's calling. He wants to give his blessings to the new kiddo."_

_John and Sam looked to each other, and rolled their eyes. __"Alright Major… put him through."_

_Ladon's voice came in soon, and it was obvious he was trying to keep his voice gentle, probably thinking he didn't want to annoy a baby. __"General Sheppard, Colonel Carter. I hear from one of our ambassadors that you've got a 'little bundle of joy' as your people say."_

_Sam chuckled, at least Ladon was trying. __"Yes Ladon…. Baby girl."_

_They could hear Ladon sighing in what could be construed as contentment for them, but John just figured he was being a drama queen.__ "Ahhh, It's a safe bet she's as beautiful as you are Colonel Carter."_

_John growled softly, and spoke in a polite tone.__ "Careful Ladon, She knows I'm a jealous guy."_

_Sam used her elbow to hit John softly, and the child in her arms stirred and murmured something. __"See what you made me do?"_

_Ladon was oblivious and continued talking. __"So have you chosen a name yet?"_

_John snickered and kissed Sam behind her ear. She sighed in relaxation, just laid her head down to rest. John replied for her. __"Well Ladon… me and Sam have talked… and we've decided on Evelyn."_

_Ladon chuckled. __"A beautiful name, what is the meaning of it?"_

_Sam cradled the child and replied. "It means life Ladon. The beginning of life." _

"_A finer name could not be possible. The blessings and well wishes of all the Genii go to Evelyn Sheppard."_

_John felt the conversation was over, and he wanted to sleep. Even if it was here in the infirmary, and even if Carson would take his baby and put her in a crib for safety, he still wanted to be alone with his wife and daughter. __"You've our thanks, and thank you for the call Ladon, It means a lot to us."_

_Ladon's voice became diplomatic, and he spoke quickly.__ "Ah yes, well there is one more small matter. I've sent a package through the gate. Compliments of the Genii."_

_John furrowed his brow. __"A package? What package?"_

_As if on cue, Lorne arrived with said package. __"Here we are, sir. Security wanted to sweep it first. Kinda jealous to be honest."_

_There in the package, a basket of some sort, were…_

* * *

"… a package of toys! Traditional Genii toys from his own youth!" The man spoke quickly, hoping it was enough.

John kept silent, the memory seemed fresh in his mind, and he could remember exactly how it happened. He eased a bit on the man and muttered. "How do you know that?" Besides the crystal clarity of the one memory, he had accompanying feelings that despite Ladon's gift, it wasn't common knowledge. "Tell me or I'll break your neck."

The man groaned as John retightened his grip. "Ladon told me! He told me as much as he knew about your people! He knew that if I ran into one of you I should try and help you! Please!"

John kept growling, but that little voice was telling him to let go, to trust this man. His brain was telling him the coincidence was too great, that it was most likely a trap and he should just shoot this guy and be done with it.

John decided to listen to the voice, as almost no one knew about his daughter outside of Atlantis and Ladon's inner circle. "Alright, I'm gonna give you one chance…" He let the man go, and quickly backpedaled keeping the gun on him. "What were you sent here to do?"

The man rubbed his sore neck, and picked the wrench back up from the ground. "Ladon sent me because Kolya's been working on a nuclear program. Even if it's not as efficient as the ones your scientists have helped us with, it's still too dangerous to let him finish them." John instantly got an idea. "How finished are the nukes Kolya has?"

The man smiled instantly recognizing the plan. "I've been able to keep them from putting together the last components but it wouldn't be difficult to set it to overload. They're almost finished."

John smiled slyly. "Lead the way, and don't try anything."

The man nodded, and took point. He led John down hallways, and John was reassured when he used military hand signals to tell him to hold while guards rushed past. John preferred not to engage them and instead remained stealthy.

It wasn't long before the man halted, using his raised fist to tell John to stop. After unlocking the door he turned and muttered softly. "There's always a few guards in there. They're heavily armed."

John smacked his lips, and looked to the man. "Any way of dealing with them you know?"

The man bit his lower lip, and then nodded hesitantly. "I can try and lead them off."

John didn't like that idea much, and instead offered his own. "How about I just do this?"

He moved in without pause and moved into the lab. The memories that had come back to him told him plainly that his reaction time was much faster, and in situations like this, his adrenaline would keep him on top.

John swept the room, and saw four guards with assault rifles and shotguns, they noticed him immediately and began to aim. John pulled the trigger once at the nearest guard and didn't wait to see him go down from the chest shot. He dove behind a desk, going prone to see out the bottom.

From his covered position, he felt the smattering of rounds impact above him, the debris from the wall raining down on him. He took careful aim and fired on the legs of the two Genii soldiers he could see from under the table. As soon as they hit the floor, he finished them off with the last of the clips in his guns.

Hearing the other Genii soldier move in closer, he shot up and using his shoulder, upended the table and sent the stacks of paperwork and doodads up like a fragmentation grenade.

The unhurt Genii Soldier was momentarily confused, but even as John drove his chain wrapped fist into his face, he fired off a burst from his rifle into John's side knocking the Atlantean down. John groaned in anguish, and managed to crawl over to the wounded soldier and get into a wrestling fight.

It was brutal, and the Genii soldier wasn't above hitting John in his wounded side to take him down, But John quickly turned the tables by forcing his chain wrapped fingers into the man's mouth, and with such a good gripping point, slammed his head into the ground over and over with a pulpy smack.

He didn't stop there though, hearing the first soldier he'd shot crawl to where he'd dropped his weapon. John picked up the rifle from the soldier he'd just killed and took aim.

He fired before the wounded soldier could turn, and saw spurts of blood rain down around him as the heavy rounds tore him apart. His body splattered to the floor in a midst of its own gore. John groaned loudly and held his side as the nanites reformed his damaged body.

The spy entered the room and looked at the devastation, and the still bleeding wound on John's side that slowly receded. "Alright, your equipment is in that locker over there!" He pointed to it. "I'll get to work on the nuke, but we won't have much time."

John winced in pain, and limped over to the locker, the pain was dulling, but so were his senses. Maybe he'd lost too much blood, or maybe the nanites were running out of juice, be he wouldn't be able to last much longer at this level of intensity.

Opening the locker, all he found was his P90E along with his ammo and radio. His vest and armor was gone, and instead he found a Genii equivalent. It was no comparison to the Atlantean made armor, but it would deflect a bullet or two if he got lucky. He slung it on and racked the first round into the small deadly weapon. He flicked the safety off the plasma emitter as well and prepared for heavy action.

He walked over to where the spy was working hard on what looked like a giant water tank. John amusingly recalled where the name for the main battle tank had originally come from. Except this tank could create a lot more devastation. "How big is this bang gonna be?"

The spy pried off a panel on the side, and quickly began to work in the inner workings. "It's been estimated around 10 megatons. Nowhere near what you guys can make, but it's more than enough to turn this place inside out."

John heard the little voice in his head again, the one that told him not to kill, only now it was telling him to be distrustful. He blinked hard and tried to make sense of the situation.

His memory was almost back to normal, and his cognitive functions were improving. He realized something, something that the little voice was telling him. "Hey, why didn't Ladon ever tell me Kolya was still alive?"

The spy shook his head. "He didn't know until recently, the Brotherhood you stole that ancestral idol from nursed him back to health. He's been with them until now because you hurt him so badly. We all thought he was dead too according to reports. He only came back on our intel a few months ago."

John didn't like that answer, it was almost too easy and it didn't make complete sense. Wasn't this guy a nuclear technician? How would he know intel like that? He carefully stepped out of range of the man. "How long have you been here?"

The man kept working, but despite now frowning, answered. "About 6 months. I infiltrated through one of his recruiters in the Genii Army."

John couldn't help but feel too lucky to have found this man. He needed to be sure. "Pretty big coincidence I run into you."

The man stopped working and let out a gasp of frustration. "Look I know you don't trust me, but I hate Kolya and I went looking for you. The guards told me you were coming and to run so I did the opposite and found you. Happy?"

John wasn't happy. It was too clean and convenient. But from what he could tell inside the machine the man was putting it together. So he stayed silent and tried to think.

He looked around the room and examined several graphs, tables, and workstations, mostly physics stuff.

The voice inside him screamed, something was wrong with the situation and he needed to regain control.

Without thinking, he walked back towards the spy. The man finished working on the nuclear weapon and closed the panel. "Alright, I've rigged a timed detona…" The click next to his head warned him that John had the pistol at his temple again. He sighed emphatically. "I thought I proved my point."

John knew what to ask now. It was so obvious. Ladon always used a headset. "Who's my daughter named after?"

The dilation of the man's eyes, the quickening of the pulsing vein gave him away. "What?"

John pulled the hammer back and dug it a little deeper into his head. "Ladon knows the meaning of my daughter's name. If he really gave you information, you'll know it too."

The man took a deep breath in, stared down the barrel, and spoke softly. "Evelyn… After your mother."

John smiled, and the man breathed a sigh of relief. John kept his voice calm. "Wrong." John raised the butt of the pistol up and whipped the man hard across the face. He reeled back and cried out in pain. John grabbed a cord of wire a few feet long, and reaching down began to garrote the man. A few seconds of choking, blood spilling down his jumpsuit, and John lessened his grip. "Talk!"

The man choked and drew in staggered breaths, he held his throat to try and stem the bleeding and once he recovered enough, replied as John put his foot down on his chest holding him down. "Ok ok! Ladon didn't send me. Kolya's got my family, I'm one of Ladon's researchers and Kolya made me work on this. Please, I was there with Ladon when he sent you the basket and I really do want to help you, but I didn't think you'd believe me…"

The voice in John's head told him it was believable, and now that the bomb was active, it didn't matter. "Alright, how long is the timer?"

The man was having trouble breathing, but was sobbing now. "Once you press the detonator… it'll be 20 minutes before it blows. That's more than enough time to reach the Stargate!"

John had one final demand, he noted the detonator was pretty much just a switch. "How do I get out of this base? If you tell me… you just might see your family again."

The man finally moved away from John, although he still stared at the gun pointing at his head. "Go to the end of this room, there's a direct elevator to the main amphitheater. Once you're there, you need to go back through the cell area and you'll find the main elevator."

John breathed hard, he could feel the rage flowing in his veins wanting to kill this man. But the small voice within him was still there. It still begged for the life of this man who had pretty much given him what he needed to escape. John finally acquiesced and tossed the pistol to the man on the floor. "Get the hell outta my sight. If I see you again I won't hesitate to fire," John clicked the detonator, and he heard a ticking sound from inside.

The man nodded and grabbing a rag from the table, put it against his still bleeding neck and shambled out of the room. John kept the P90E close to his chest, and ran back to where the man pointed out.


	7. Acceptance

**- Chapter 7 - Acceptance-**

The elevator was right where the spy had said, and John tried to catch his breath. It was likely there were more Genii soldiers guarding the exits and looking for him, With the P90E though, he had much superior firepower.

It proved itself rapidly, as when he entered the Amphitheater there were three soldiers there, although they weren't expecting him.

He could almost imagine it, the grating of the elevator rising and John, with chains hanging from his wrists, blood stains on his skin, and no shirt with torn pants and boots. The Genii vest looked primitive, almost roman. He must have looked like a demon as he raised the P90E and tapped the trigger.

They hardly had time to react, the armor penetrating rounds easily defeating the weak Genii armor. A few got shots off but none hit John. He stepped forward, and then instantly fell back as a pair of shots hit his chest knocking him down from some unseen assailant. He groaned in pain and rolled to the side behind cover as more shots landed near him. _"Sheppard!"_

Kolya… it figured. John drew in a few sharp breaths and finally relaxed as his chest reformed from the nanites. He fired a burst of suppressive fire and screamed. "Kolya! You've got 18 minutes till this place turns into radioactive slag!"

Kolya growled and moved closer. "Are you trying to convince me to leave?"

John smiled, the anger within him felt so good as he flicked the safety on his rifle to plasma. "No! I just want you to know that I'm gonna enjoy killing you before it blows!" He rolled out from his position and fired. The pulse of plasma was absorbed by the Lantean Armor Kolya now wore, John's armor. He groaned slightly from the heat, but took cover as well as he fired again.

The bullets landed next to John, blinding him temporarily as he crouched behind a chair. "I'm gonna rip that armor from your body you slimy cocksucker!"

A staccato of fire and falling splinters around him warned that Kolya had a good automatic weapon as well. "I admire your tenacity! But only one of us will walk out of this room, and I have much I must deduct from your life!"

John popped out from the right side of his cover and fired a burst. The bullets shattered a TV screen above where he thought Kolya was and showered the area with glass. Kolya cursed and blind fired suppressing John again. "Come on Kolya, you're gonna die and you might as well meet it honorably!"

John felt something skim across his cheek and winced, lucky shot. He groaned softly as the skin reformed. Kolya screamed and kept firing. "As long as you die as well, I will gladly meet my end!"

He took a deep pair of breaths, fired a blind burst from his right to distract Kolya, and rolled to his left. From the prone position he fired the plasma beam again, only instead of targeting Kolya, he aimed for the wooden desk he was hiding behind. It instantly set alight and began to smolder into a heavy smoke. John got up and began to fire blind through the smoke. Emptying the clip into the general area Kolya was in, he rushed in and tossed the empty rifle to the side.

Kolya was coughing and trying to move through the smoke. John didn't hesitate and tackled him into the wall. Kolya fought back with an elbow to John's face as he tossed his rifle to the side as well. "So you ARE half honorable! Come then! Kill me if you can!"

John was only too glad to oblige. Recovering from the elbow strike, he rushed forward in a low bull rush and picked up Kolya like a football player. He slammed him into the wall and drove fist after fist into Kolya's gut, his armor tearing the skin off John's knuckles. He ripped downwards, unzipping the armor and spinning Kolya around even as he countered. The smoke blinded him and the intense heat of such a close fight and the smoldering wood made his skin slick with sweat, Kolya's too.

He felt a sudden stabbing pain in his back. John should have expected Kolya to fight dirty in an honorable fight. He fell back and groaned as the nanites now struggled to push the blade from his back, dangerously close to his spine. John needed to kill him, now.

Kolya jumped forward and slammed his heavy body against John sending him to the ground. The knife twisted in John's back and he howled in agony as the serrated blade tore his insides apart. He felt the massive surge of adrenaline push him over the edge, and in a manner similar to a pushup, knocked the heavier Kolya to the side with his elbow, ripping the armor from Kolya and finally giving himself a chance to pull the blade out, landing beside him with a clatter.

John was hurt, his breathing sharp and vision blurry. He felt the agony of his body cry out for respite. But Kolya was getting up and this needed to end now.

So John jumped forward, gave Kolya a hard right hook to his face, then a chop to his neck. The old soldier's eyes nearly popped out of their sockets as his larynx was bruised, and he doubled over in shock, landing on his knees with his hands to his throat.

John grabbed him by the collar, and seeing the still smoldering wreck of the desk, the burning sensation of the smoke in his eyes, and the pure hate in Kolya's face, John lifted him up into the air from the neck despite his body protesting in every way possible. "I said I'd enjoy killing you."

A memory flashed across his mind, and similar circumstances.

* * *

_"No! Please you cannot take the sacred icon!"_

_John shrugged and handed the ZPM to McKay who eagerly secured it in his pack. __"Trust me, It'll serve a much higher purpose with us than sitting around gathering dust." The Brotherhood Acolytes, men and women who worshiped the ZPM stood between John's team and the Stargate, they didn't look happy._

_To the side, Kolya and his 2 men were angered as well. __"Have you no heart Sheppard? I could tell you were ruthless on our first encounter, but to steal their faith?"_

_John growled at Kolya, god he wished they hadn't taken their guns in exchange for getting outta that hole. Then again the Genii weren't armed either so…__ "Who cares about faith? The only thing that counts is the Wraith…" John's smile was devious. "Hey, that rhymes!"_

_The others on AR-1 weren't so perky. The prospect of a ZPM was good, but to anger these people didn't seem right. McKay stayed silent and inched away from the angered Genii Soldiers along with the Brotherhood acolytes._

_John didn't care. After facing the Wraith a few angered villagers who didn't even know the value of the technology they worshiped was a small price to pay. He looked back at Ford, none of them with weapons.__ "You ever get into a bar brawl Ford?"_

_The instant John turned his head, Kolya produced a knife from his sleeve and lunged forward. Teyla tried to jump ahead to push him, but it was too late._

_The knife hit just an inch above John's heart, the Genii Soldier's aim excellent. He wasn't expecting the typically underdressed John to be wearing his stab vest and Kolya hurt his wrist from the sudden jarring stop._

_John reacted as he rolled with the blow, and grabbed Kolya's wrist and spun it around. Teyla and Ford charged ahead, using their fists and feet to fight off the other two Genii who moved in to attack John and McKay as well. Rodney backed off, unsure of himself in a fight but quickly got in a tug of war with one of the Brotherhood Acolytes who tried to take the satchel with the ZPM back._

_It degenerated into an all out brawl, Teyla easily dominating anyone who stood in her way and Ford having less, but still significant success. McKay used the ZPM to whack the acolyte on the head and instantly began to run back towards the gate._

_John and Kolya were almost evenly matched, Kolya knowing instinctively to duck and shrimp out of John's grasp. John countered and they entered a martial arts parry, neither willing to back down._

_It was an odd sight, the graceful brutality of the two men trying to kill each other. John blocked, felt his own punch get blocked, then ducked and spun to avoid the blade again._

_Each hit was a jarring impact, their bones ached as muscle and sinew smashed against each other in what seemed a titanic struggle. John was faster, but Kolya was stronger and armed. John repeatedly tried to unsheathe his own knife, but Kolya kept pressing the attack and forcing John to duck, block, and weave out of the way._

_They were well away from the main scuffle now, no one willing to get close. Ford and Teyla were covering McKay's tactical retreat now, following John's scream of __"Run!". John didn't care if he did get stuck on this planet. Kolya had killed four of his men, tried to have John killed, tortured McKay, and he nearly killed Liz… Kolya was going to die and it was going to be today._

_John feigned a weak spot, and seeing Kolya go for it with the blade he quickly countered and grabbed his wrist again, his own forearm getting nicked in the process._

_Kolya saw it coming and there was nothing he could do about it. None of the others in the scuffle were badly injured, but when John flipped Kolya around, and put one hand over his mouth to control his head. Everyone knew what was about to happen._

_Using Kolya's own wrist, John spun Kolya's arm around and slammed the knife into his chest. John spun him around again, twisting the knife as he moved and came face to face with the old Genii soldier. He didn't make a sound, his mouth still covered by John's hand. His eyes were wide and at this range, John could see the tiny blood veins constrict, the black irises begin to cloud over._

_John took it in for a moment then yanked the knife out. Kolya's blood spewed, covering John's vest in the dark red fluid. Kolya wheezed as John let him go and back pedaled away._

_Kolya fell to his knees, clutching his chest where the open wound bled profusely. He spat out a mixture of blood, saliva, and mucus as he coughed and finally fell flat to the floor on his face._

_Everyone was silent for a moment. Up until then, blood had never been spilled on Brotherhood land. The Acolytes nearby looked at John as if he were some unholy demon. Their eyes burning with hate._

_'Time to go' was all John could think about._

* * *

Kolya spat in his face, and suddenly howled as John slammed him into the edge of the desk, the blunt side clearly breaking the heavier man's spine upon impact. Kolya screamed out in agony as a large splinter shot through his side and penetrated him completely, but his legs stopped working, the spinal cord severed from such a savage attack.

John lost control. There were maybe 15 minutes for the bomb to go off but the irrational and purely animalistic urge in his body yearned for retribution, He'd killed this man before, and for some reason he just wouldn't finish dying.

So he loomed over Kolya, curled his fists, and began to punch relentlessly. The first hit broke his nose, snapping the cartilage and giving him a broken look. The next tore skin off his brow which now hung limply exposing the flesh beneath. Another pair of unrestrained strikes and some of Kolya's teeth dislodged and fell to the ground. Another trio of hits and John finally stopped, Kolya coughing and choking from swallowing teeth, blood, and his own torn flesh. His cheeks grew puffy and bruised, his eyes shut from the intense pressure they'd just endured.

Both men had torn flesh, but only one healed quickly, and soon John had had his fill of the violent revenge.

Kolya was still conscious though, and John could barely make out his voice amidst the crackle of the broken screen behind him, and the sizzle of the vest on top of the smoldering desk. "Kill me, take your revenge."

Now that he was there, his eyes burning from the smoke. His back still aching from the knife wound, the prime target of all his hostility lying three quarters of the way to death on top of a burning wooden desk…

The voice inside his head faded, and all that was left was a suggestion, no longer an order. "They say revenge is best served cold… shame you're a tad overdone for my taste."

With that, John calmly walked over, picked up the P90E from where he'd dropped it, reloaded the rifle, and left Kolya to wait for either the flame beneath him to kill him, or for the nuclear device set to explode. His voice carried, in a tone John had never heard before… pleading. "What, no… Kill me Sheppard! You're a brutal cold blooded monster! You can't leave me like this! Kill me! Please! KILL ME!"

John ignored it, and set out in the now familiar hallway, Kolya's voice faded, and soon his pleas for a mercy killing were nothing but dust in his memory.

It wasn't long until he reached the cell block where they'd held him. John had the instant thought that Todd was still there. Proving his thoughts, the raspy vibrating voice of the Wraith flowed clearly. "Sheppard!"

John reached the cell where he'd been held, and across from it was Todd. He had an odd look of surprise, perhaps wondering what to say in such a situation. John simply smiled and looked to him. "So hey, how would you like to be a mine worker?"

Todd growled, and reached out as far as he could, well out of reach of John. "I would sooner die than…"

John interrupted. "I thought you'd say that." He held the P90E to his hip, and held the trigger down. The bullets peppered into Todd, pushing him back into his cell amidst spurts of his thick bluish blood caking the floor and bars of his cell. Even after taking a full clip from the P90E, he still drew ragged breaths and looked to John. "I expected no less…."

John shrugged. "Since you're about to die anyway, I might as well tell ya. Nanites." John flexed his arms, posing for the Wraith. "Kinda hard to feed on someone who's half machine."

Todd grimaced, and spat in John's direction. "You **are** an abomination."

John raised the rifle at Todd's head and switched to Plasma. "And I finally get to kill you… Dunno why, but I get the feeling I should have done this a long time ago."

Before Todd could reply, the hot stream of blue plasma bored into his face cleanly bisecting the Wraith's skull. It felt oddly good to kill him outright instead of leaving him to die like Kolya… almost respectful in a way. John didn't bother to watch and kept moving. He was having a hell of a day, and there was only a little more than 10 minutes before this place turned into a smoking crater.

There weren't anymore guards. It surprised John. Apparently everyone had either left, or was there were fewer people on the base than he'd expected.

John turned into the main corridor that led to the main elevator, he held his rifle up and instantly noted a figure standing in front of the doorway. The slender and somewhat short stature gave her away instantly. "So Sheppard. You've killed just about everyone I've ever loved."

John kept his distance, no telling what the bitch had on her. "I'd say I'm sorry, but most kinda didn't give me a choice."

Sora growled, and showed a metal staff in her hands. "Not my father… you saved your own hide at the expense of his life."

John remembered what happened in the hive, but he also saw doubt on Sora's face. The feeling inside him begged to know, even if it would only take a minute. The other part of him told him to shoot, as that minute could be used to escape the soon-to-be atomic blast. "Is that what Cowen told you?"

The P90E was up, aiming right at her head. The same urge to shoot was there, but this was surprisingly controllable, almost as if something else was holding him back. But it felt right, it felt internal and completely normal. This conversation was filled with memory he didn't know he had, and even more, diplomacy John didn't know was inside him. Sora snorted and gripped the steel shaft harder. "You left him to die, along with Alwin. That's all I needed to know."

John shook his head and scoffed. "Like you can believe Cowen, Your father didn't give me a choice! I told him to go if he wanted but instead he put a gun to my head!"

Sora now had a tear going down her cheek. Her moves were hesitant, almost repentant. John saw the opportunity, god he wanted to shoot her so bad but now, to actually convince her to let him go, maybe even _help__ him_. "No! No you killed him! You shot him because he was in your way!"

"I shot him after telling him **twice** to move! He could have put the gun down and come with me… He didn't and put the fucking gun to my face! If I hadn't shot him, none of us would have made it out of that hive!"

"You, you're a monster. You've killed so many people."

This couldn't take much longer. Less than 10 minutes to get the hell out of here and far far away. The final nail in his argument came flawlessly; John was surprised by his own words. "Listen Sora. He had a choice. He made the wrong one. Tyrus was a good man but he made a tactically bad decision. Don't make the same mistake!"

Sora was shaking now, her rage was laced with what looked like hesitance, and John felt no shame in exploiting it. Though a part of him questioned why he didn't just shoot the bitch who'd taken such pleasure in bringing him to within an inch of his life. "And what do I do then? Join you? It's all over for me Sheppard. You won. You're an ancestral monster and you're right. You've saved this Galaxy from the Wraith and I still hate you! So what am I supposed to do? Just let you go and pretend this never happened?"

John shook his head, and sighed as he lowered the weapon. "Disband the rogue Genii, rejoin your people. I'll tell Ladon to cut you some slack… You can be with your people again."

Sora sniffled, the anger still in her tone. "You'd do that? Even after I…"

John sighed, and finally pointed the gun away from her. "I'll be honest. I want to kill you **so** bad right now. Just leave you lying in a pool of your own guts… I want to do to you what I've done to Kolya…" He swallowed. "But I've killed enough today. Sparing a life is harder and well… it's starting to make sense to me."

Sora seemed to drop her defensive stance as well, and after wiping the tears from her eyes looked up at him. "…Go, I'll clean things up here."

John felt an unbearable urge to just let her stay, let the problem fade away into radioactive vapor. But the feeling inside him spurned him to action. "No… you need to leave now. Take anyone you can, the bomb Kolya was working on downstairs is gonna blow in less than ten minutes."

Sora's eyes went wide, and she visibly flinched. "_By the ancestors. _You _bastard!_ You…"

John waved his hand in a negative reply and began to inch towards her. "Forget hating me! I hate your guts too but I'm looking past that! Think about yourself and your people! Get them out _now!_ Make the right choice!"

They inched around each other, like two wolves getting ready to attack. John reached the elevator and pressed the call button. There wasn't much time left. Sora waited as well and kept her breathing calm. "I'll go… but if I ever see you again I will try and kill you. Mark my words."

John shrugged as the elevator doors opened, both of them stepped on with their weapons pointed at each other. "Ditto."

The elevator began to move quickly and Sora gave him a confused look. "What? That some kind of insult?"

John chuckled, and keeping the P90E at his hip shook his head. "Nah… means I'll do the same to you." the elevator moved fast, and it wasn't long before the reached the top floor. "So don't take this the wrong way, but if I ever do see you again, don't be offended if _I_ try and kill _you_."

Sora snarled back at him. "Well like you said…" she stepped out of the elevator and moved into the forest towards a barracks. "Ditto."

* * *

John didn't bother to wait for Sora, and instead followed the path to what he assumed was the gate. He only had 2 clips left for his P90E, and the battery for the Plasma Beam was only at a quarter power. A few bursts and plasma shots were all he had left if he were to get engaged.

As if to tease him, dirt began to fly up from snipers in what appeared to be watchtowers. He dove to the side and managed to avoid the fire by sheer luck, and he hid behind the tree.

Only about 5 minutes left. This wasn't good. The Stargate was probably already that far away, and having to avoid snipers would make things difficult. He took a few deep breaths, calmed himself, and carefully leaned out from the tree he was using as cover.

The watchtower was well armored, and not wanting to expose his position, he instead of firing began to move stealthily along the side of the path. His dreams of stealth were suddenly broken when a radio signal came in starling him, and alerting the guards to his general location.

He jumped back, and dove behind a fallen tree feeling the bullets landing just a little closer than he'd like. He clicked his radio and screamed into it "This is Sheppard! Who's out there!"

A familiar voice, filled with emotion he couldn't even begin to describe. _"John! It's Sam! We're in the Phoenix and heading towards the Genii complex! Where are you?"_

John froze for a second, then chuckled mindlessly. Of course they'd found him. Sam had most likely figured it out from the DHD as soon as they realized what happened and brought their new strike craft in. John had no idea exactly how much time had passed or how far this planet was from Atlantis. Knowing Lorne, they probably pulled a ZPM out of Atlantis's power grid to power the ship to the limit. Atlantis would survive, especially with the Traveler fleet still around.

Time was running out, and they needed to move NOW. "Sam! I'm on the ground a few hundred feet from the main complex in the direction of the Stargate!"

He watched as Sora led a platoon of men down the road, waving them down with a hurried scream. A few scanned the trees looking for him, but none stuck around. John aimed the P90E instinctively, but held back from actually firing. Sam's voice came over the radio again _"I've got Ronon and the marines in the hold! We'll set down near the gate, recover you, and assault the base!"_

John chuckled, _'Oh man… why is it always like this? Just once…' _"No can do Sam! I uhh kinda maybe set off a nuclear bomb Kolya was working on and in less than 5 minutes this place is gonna blow!" He waited a second for it to sink in, and decided on a course of action. "That thing doesn't have beaming tech does it?"

_"Not yet! We have to actually land to pick you up!"_

Less than 5 minutes, probably more like 3 minutes, only 180 seconds now that he thought about it. Could Phoenix land that quickly? "Drop an airstrike on these watchtowers near the gate, Land and I'll come aboard!"

"John… you're too close! We might hit you!"

"Well, I'm dead either way so just fucking do it! Danger close my ass!"

John hated to repeat his orders, especially as emphatically as he screamed into the radio. They were his orders not because he wanted opinions, if he wanted opinions he would ask for opinions. No, orders were orders were orders.

And his people knew that, as the blast of yellowish fire that suddenly streaked in at relativistic velocities detonated and knocked him plainly out.

* * *

_This was to be expected. Atonement was something that very few people ever actually achieved. Especially after a crime as severe as the one he'd committed._

_Yet this was the very reason he was still alive. To assist them, to give them the scientific push they needed in their projects. To help the others understand how technology was just an extension of the body._

_He was here now because he wanted to give them the best, the one thing the Ancients couldn't do, Project Arcturus._

_John watched from the doorway as Carson coldly treated the man. He'd already given his evaluation and it was final. 6 months and Rodney's body would eat itself away from the massive dose of exotic particles his body had received trying to get the technology to work on Atlantis. He had worked on the project alone, in his own lab several floors away from anyone else. It was the only way people would accept having him around._

_Ronon and Teyla were gone now. John couldn't blame them. No longer were they the close knit family they once were, although Ronon had wanted to stay. Now they felt like distant cousins – family only by extension. John hated what had become of this place, all because of the actions of now 2 men._

_They weren't evil, and they weren't necessarily wrong. But the pain of life had gotten under their armor and forced them to use crutches. Some form of validating their actions._

_Sam still wasn't talking to anyone about the incident. And John felt it was better that way. Sam was surprisingly strong, and in a strange way the attack had forced her to become even harder than she had been, refusing to take the easy route had proven integral to her sanity._

_John loved her now, he knew that, and as he watched Rodney run his hands through his hair and come away with a small patch of it. Well, he couldn't really care anymore. His close friend for almost 2 years, turned into his hated pet for another was now a dead man walking._

_John had promised not to kill him, instead letting him be in his own section of Atlantis where he could work on the projects that his genius would crack and help the expedition. John had intended for no one to ever see him again except those who went looking._

_That was until the city locked down. No one knew why, and for almost 3 hours they were locked in their respective areas with no way of getting out. When the doors opened, no one knew why the city had done what it did. They had to get to the control room and do a comprehensive scan to figure it out._

_That's when they found him. Dying, screaming, and convulsing from the burst of radiation._

_He'd failed again, and this time it almost cost them everything._

_Rodney died saving them. Bleeding the energy into another reality, exposing himself to the hard exotic particles his genius insisted could be fixed…_

_In a way he did serve his penance, the crime for which he should have died, never reprieved, was now meted out in his last act of saving the ones he hated to love. Perhaps the universe did want some sense of balance._

* * *

John groaned loudly, he was being dragged, again. This time though, instead of by just one foot, another pair of hands picked up his shoulders and hauled him into the landed strike craft. All that was on his mind was escape "_Fucking go!"_ his voice was hoarse, but the strength behind it was evident.

The world was nothing but a fuguish haze. Faces passed over him, worried, unfamiliar. He heard a subsonic roar, and then a much more prevalent whoosh. The Pegasus galaxy had a tendency to use 'In the nick of time' just a little more frequently than John liked, but he was safe, he was back with his family.

He recognized them now as they lifted him up onto a stretcher. His body ached, why did it hurt so bad? The nanites should fix him. His right hand came up, another soft hand holding it close to her face, her voice was criminally weak "John…."

"Hey… sorry I'm late."

He felt Ronon's strong hands lift him into a sitting position, and Teyla rub his shoulder to give him comfort. John's focus was on Sam though, who looked as if the world had just nearly ended. "_You're damn right you're sorry…!_ We'll talk about how long you're grounded when we get back… Carson?"

The Scottish doctor came close with an immorally large needle. "Stay still lad… you've been through the ringer… we'll be back home 'fore you know it son…"

He didn't feel the needle, but the sedative inside was more than enough for what the pain inside his body needed.

* * *

Frozen.

That was the only way to describe it.

A nearly inanimate state in which the cellular degradation would slow down to almost nothing.

But something told him this is what he deserved. That death was something too simple and final for the crime.

John ran his fingers along the smooth surface, along the same lines in the face of the man he once called friend.

"John."

He turned, and she was standing off to the side, watching him for an unknown amount of time. "Hey…"

Sam walked up and stood next to John, looking into the stasis pod. "You know I trust you John… but…"

John smiled, he'd finally realized why he wanted this done. He didn't understand it fully, but he knew the answer in his head. "You want to know why I ordered him put in here… so he technically stays alive."

Sam sniffled once, not in sadness, but a heated resentment "To put it nicely. I just want to know you're not doing this for some sentimental reason or else I'll gladly pull the plug."

John sighed, even he was a little astounded at his thinking. Something told him that by doing this he had saved Rodney, but now? Knowledge he never learned was telling him that this was what the man deserved… Rodney had always begged forgiveness, he said it was burned into his memory and his nightmares were the worst punishment he could imagine. "He dreams in there you know?"

Sam furrowed her brow and looked at John. "Say what?"

John shrugged, the concept was unbelievable. "He dreams, and all he has are nightmares. I left him alive so he could suffer Sam. It wasn't a merciful thing I asked you to do." He looked to Sam and held her shoulders. "You might have wanted to kill him. I wanted to _destroy_ him. Carson says he might live another few years in that tube before the cellular degradation finally finishes him."

Sam was bewildered. "Wait, you want him to keep alive so he…?"

John nodded, and sighed empathetically. "I learned something Sam… I don't know why all these thoughts came to me after the crash… in fact I can't even remember what I was thinking… just what I did. But I found that it's harder… and sometimes more important to spare a life than it is to take one. And that sometimes killing someone makes it harder to move forward."

Sam was quiet, she wrapped an arm around her husband and pulled him away from the stasis tube holding the man who had betrayed her so harshly. "Since you bring it up… Ladon Radim says that most of the Rogue Genii have surrendered. Sora and their command staff were going to be imprisoned and executed… but after your communiqué to Ladon, he's decided to spare their lives and let them live on some backwater planet. He also says he's 'profoundly' sorry for not telling you about Kolya. He says he was hoping to deal with it internally."

John scoffed. "Politics, tell me again why I agreed to this?"

Sam leaned in and set her head down on his shoulder. "Beats me, maybe Ronon or Teyla can tell you. They're waiting for us in the mess hall with Evie along with Carson and Laura."

John stopped, he pulled Sam into a hug. "What about Evan?"

Sam shrugged "He's in command right now, until Carson clears you completely."

John sighed, and then kissed Sam's forehead. "He deserves to be there too."

Sam smiled. "Yeah he does. Ford should be back soon; I'll tell him to relieve Evan when he gets here. Larrin can handle her part too."

John was silent a moment, then squeezed Sam hard. Whispering softly into her soft long hair. "I'm alright Sam, I don't really know why, but I'm alright now. I realized something, I miss my family. Ronon… Teyla… I miss us all being here." He sighed "I'm gonna make it better Sam. We're gonna be alright now."

Sam raised an eyebrow in surprise and shook her head in confusion. "I'll never understand you. But that's okay."

John chuckled and pulled her back into his walk. He needed to go see his family now, the family he'd almost lost, but were willing to risk their lives to save him.

His memories of inside the Genii facility, being tortured, and finally killing someone who seemed like such a terrible nemesis were blurred. Maybe it was his mind trying to spare him the pain. But that feeling in his head now, firmly cemented in that mercy was not a weakness, and that to convince the other side to give up was more beneficial than simply blasting them from the face of the universe.

He was glad he had that experience, now as he moved away from the stasis chamber, he felt a different sense of wholeness to him. Something akin to what he felt when Chaya shared herself.

John Sheppard was ready now. The battles and conflict of the Pegasus Galaxy were almost over, and right before it cost him his soul, the light of the universe forced him to see the weakness festering in him. The Milky Way was next… and the beginning of the war to reclaim Humanity's spirit.

The final legacy of the darkest hour of the Atlantis Expedition now stood frozen, forever locked in the eternal damnation of a nightmare of his own creation. No one would ever save him, no one would ever see the humility he'd learned, and no one in this galaxy would ever want to mention him again. The lessons learned by him would go on though, transferred into another, more worthy subject, while this one relived his personal hell.

* * *

_No one… it's… wow… the hell do they make this stuff out of?_

_I need to talk to her… god just talk to her… make her see… it's wrong… it hurts so bad…_

_Sheppard… everyone loves him… he's a monster. How can I show her? I'm all she needs… I'm here for her… I'll kill for her…_

_It's only fair… I love her… she should love me back… I give everything I can… I've lost more sleep than anyone else because of her… and I'm happy to be there for her…_

_She's mine… why'd you do it Sheppard? You cold blooded bastard._

_Control… she knows you're drunk… she's laughing… stop laughing! I'm being serious… I'm telling you what I feel…_

_Everyone laughs… I'm not a hero… I'm not a soldier… I'm the fucking genius who keeps them alive and they laugh! They'd all be dead a thousand times over if it weren't for me!_

_Just because she smiles and pretends she's ok doesn't make her better than me… it makes us perfect for each other… but she's not better than me… I've waited so long… it's been a hard road but the fairy tale is almost done… I'm so glad it's coming true now…_

_God I could be everything for her… we've lost everything… I want to hold her… I want to kiss her and make it all go away… she'll kiss me back and tell me she loves me… she loves what I do for her…_

_You don't get it do you? You just don't understand… Life is a miracle Sam… I know you think there aren't miracles anymore but everything is a miracle! I love you Sam! Ever since you showed me what a moron I could be… you're the only one who could ever complete me… stand up to me and win…_

_He hurt you Sam… Sheppard's the same… I don't know what they did… but I don't care… because it doesn't make a difference to me! He's a monster who'll hurt you… I want to heal you… I want you to know I love you… I'll fight to the end of the universe, I'll bring the stars down from the heavens themselves, I can't get you out of my mind Sam… We're all sons of bitches now and I just want to help you feel alive again. I'm a man of science and they're men of action… we both have mystery around us…_

_I've thought about you unceasingly… My entire soul is engulfed in love with yours… I get butterflies in my stomach just seeing you smile._

_Don't fight this Sam… don't push me away… you're confused Sam… it's been so long since you've been loved that it feels strange I know… All they want is your body… I want to share our souls…_

_You love me… you care for me… but you love him… and you care for him too… Why? Why are you paying from your very soul to get that… when I can give it to you now… no price…_

_No problem can be solved by the same level of consciousness that created it… you know this… why… why are you doing it again? Why are you torturing yourself…?_

_It's for your own good Sam… I want to take care of you… no one else knows… no one can stand to think of it… I don't want you to fight it please… you'll come out better…_

_It's a cruel life we have Sam…. And we have to know our limitations… we can't be superficial anymore… we can't be fatigued… we have to cling to what's close to us… never let it go… we have to hold onto the last bit of what we can do…_

_I just want to make it better._

* * *

_Major Ford had been a bit lethargic in coming to see what Colonel Carter needed a hand with. Something about a generator she had just fixed. It was late anyway and General Sheppard and Colonel Lorne were busy in a meeting. 'Sides, he'd always had a nice friendly relationship with Sam and John._

_Ford had offered to to this just because he was close by. Normally a marine would be around with big burly muscles to do the grunt work, but Sam hated having guards in the room with her and dismissed them._

_He heard a crack, as if a bottle had broken. Ford rolled his eyes figuring McKay was in there, and in his bumbling love sick form had knocked over some highly expensive and rare technology that Sam was chewing him out over._

_The man was so strange, obviously a genius, but a complete social dingbat. But Ford didn't care, he was a good friend who just acted foolish sometimes…_

_What he saw as he entered the lab wasn't a fool at all. Instead what he saw forced his throat to constrict in shock._

_It was only a moment he hesitated, but Sam's groan of pain and then terrified plea to stop was all that he could hear now. Ford rushed forward and without a word, but a scream of rage, dove over the table knocking a stack of peper over as he tackled McKay off her._

_He was already bleeding and bruised, she'd put up a hell of a fight. But the broken bottle and bleeding wound on her forehead told him what the crack he'd heard earlier was._

_Aiden wasn't an angry man, he'd seen suffering, suffered a lot himself, but he kept his heart as true as he could, He's heard from Sheppard what happened at the SGC, and he gladly helped Sam with anything she felt she needed._

_McKay was obviously infatuated, obsessed with her. But to do this… __Aiden wasn't an angry man, but the savagery of the beating he gave McKay now would fool even his closest friends._

_There is some truth in that saying… those who fight monsters, are at risk of becoming monsters themselves._

* * *

**Epilogue**

When John Sheppard had stopped thinking of Earth as home, he never expected the next time he'd be there to wake up in a prison cell, if he'd known that, he would have kept a few doodads at the SGC to pass the time.

The past few days had been a grueling nightmare. All he really remembered was the slow recollection of his memories, who he was, and how he ended up in this cell.

He'd tried to kill Woolsey, he clearly remembered taking the shot. Even as the man watched him being pulled out of the Jumper with concern, John had drawn his sidearm and taken a snapshot.

It wasn't a fatal wound, and Woolsey was apparently a little tougher than John had given him credit for as the politician gave a manly scream of pain instead of the girly whine of agony he'd expected.

McKay hadn't been much better, the two of them suddenly becoming arch nemeses and trying to tear each other's throats out. Dr Keller was well out of her league in treating them, and under lock, key, and guard, had shipped them back to Earth for treatment at the SGC where Samantha Carter along with Dr Zelenka, Dr Lee and Dr Lam would figure out what happened.

John now remembered who he was, and the Brigadier General he'd seemingly been turned into was gone. Forever reduced to nothing but strange half-recollections, and the faint trace of feeling in John's head. Video recordings were the only tangible evidence of his ever existing.

There was always a guard right outside the door watching him. For awhile they even watched him go the bathroom, thankfully giving him a little curtain to give him some semblance of privacy.

Interrogation after interrogation, never really figuring out what was the matter. Eventually he began to agree with them, not because he'd broken, but rather he'd come to his senses.

Finally, after almost 4 days of this agony, he felt back to normal. His memories back intact, yet the hint of something inside him remained. It was so obviously not him, but at the same time he drew some comfort from it.

It told him was that the Wraith were due for an asskicking, and he would gladly provide it now. The other feeling inside was something he ignored… at least until now.

The door to his cell had a little sliding window in it, and he heard the latch being released. He'd been bouncing a ball they'd thankfully given him so he wouldn't die of boredom, and taking a final throw, he looked up at the slit.

"Colonel Sheppard?"

He recognized the voice, Familiar, friendly. and for some reason…"Colonel Carter." He caught the ball and straightened as she looked through the slit. "I think I can safely assume you know damn well it's nice to see you again so soon, so I'm going to skip right ahead to 'I'm really hoping you're the one they sent to tell me I'm back to normal.' Because I'm about to die of cabin fever."

Sam smirked, and the other latches to the door opened. He watched her enter the room, a guard with his Zat ready to fire blocked the doorway. John couldn't help but feel a little offended. "What's with the muscle? I really do feel a lot better. Dr Lam has already given me the go that I'm me again…" Not that she would have much trouble fighting him – she wasn't a small woman.

Sam sat down on the bench across from him and shrugged. "SGC rules. Can never be too safe" She sighed, but with a sign of relief. "It is good to see you again John. Despite the circumstances."

John sighed, and rubbed his face to try and show his frustration. "Yeah well the real John Sheppard just stood up. I'm a Lieutenant Colonel, Military Commander of the Atlantis Expedition… Not Brigadier General John Sheppard, Renegade and rebel leader of a stolen Atlantis trying to kill Darth O'Neill."

Sam drew in a sharp breath, more out of restraining her laugh than shock, and motioned for the guard to leave. "It's okay Sergeant. You're dismissed."

The sergeant was reluctant, but with a slight sigh he followed orders. But not before informing the guard outside to keep good watch.

John clenched his fists a few times, and figured he'd get the awkward part over first. "Thanks. Uh, listen; I know what I may have said before…"

Sam waved her hand dismissing him. "It's okay John, We still don't know exactly what happened but from what we can tell, the Jumper's mental interface was affected by the magnetic disturbance on that planet. The ship was shielded against it, but for some reason your consciousness's were imprinted with your alternate selves. We don't really understand the science of it, but we've seen the alternate realities part before. As far as your consciousness, it seems sort of similar to what happened to you and Dr Weir back on Atlantis with the escape pods a few years back."

John groaned dejectedly. "Oh god, don't remind me. Caldwell still brings that up when he's losing an argument." He gulped, still trying to get over this hump. "What I actually wanted to say was, well… I know it wasn't me. Another reality, another universe maybe. But I… you and me… " He froze and looked at her in the eyes. "Help me out here would ya? I got no clue what I can possibly say here."

Sam tensed up as well, she didn't feel quite as comfortable as she was when she entered. "Yeah um, your 'other' personality had some trouble with that."

John rubbed the back of his neck and tried to look apologetic. Dammit it wasn't him! "Yeah…"

The awkward silence between them was excruciating. Neither really wanted to explore what the 'other' John Sheppard had talked about them just yet. Sam finally couldn't take it anymore and spat out quickly. "Woolsey's alright, just so you know."

John breathed a sigh of relief, both for Woolsey and for getting past the awkward bump intact. "That's good to know, I've already killed one commanding officer and I'd rather not make it a habit." The expression Sam gave was priceless, and he winced as soon as the dark comedy left his mouth. "Sorry."

Sam smiled politely, and somewhere deep in her mind she remembered what the 'other' John Sheppard had said during the questioning. "Um, yeah."

John smiled politely too, he remembered what the 'other' John Sheppard had said as well, but only because he saw the video they took of him. "Yeah, I'm boned aren't I?."

Sam nodded gingerly, she loved Futurama as well. "You could say that." She waited a few seconds to continue. "But, you seem to be back to normal. So since it wasn't technically you who tried to eviscerate Woolsey the proletariat." Sam took a deep breath in, looked out to the hallway, and let it out. "Look John. I know what you wanna say… Don't take this the wrong way, but in a way I'm sorta glad it was you that, you know… I know that it's not our reality and none of us really knows if what happened over there will ever happen here… But I think apart from Doctor Jackson…"

John let a groan of frustration out and tugged his hair. "Oh god, General O'Neill's gonna kill me isn't he?"

Sam snorted in laughter, stifled it, and looked to him. "Oh yeah. But he'll hold off as long as you head back to Atlantis as soon as the Daedalus is ready to go."

John shook his head as he palmed his face. This was by the far the most awkward situation he'd ever gotten himself into. If it were at all possible he'd go and kick his bearded evil Spock twin's ass for putting him through this. "Did he get the full report?"

Sam nodded. "He said it makes sense… He'd **have** to be insane to try and become President. He hates politics."

"Well, that's a little better than I hoped."

"In fact he asked me to tell you that he'd be glad to invite you out for some talk and cake. That is if you don't think he's a fascist megalomaniac and are going to try and, what was it you said? 'Tear his ass out through his mouth?'"

John groaned again and buried his face in his hands. "This is never gonna go away is it?"

Sam shook her head, and leaning forward, gave John a pat on the shoulder. "Probably not, but don't worry. Welcome to **my** life."

John looked up at her with a surprised expression. "Uhh, come again?"

Sam shrugged. "I've seen enough alternate versions of myself to know I shouldn't worry about what they've done or…" She didn't say it, but she knew damn well what most of those realities ended up trying to tell her. But just like the reality John had just seen, and the one she'd visited not too long ago, it was more a matter of physics than fate.

John gulped. "Uhh, yeah, Well, I'm sort of an alternate reality virgin here so… be kind?"

Sam again stifled a laugh, and palmed her face in embarrassment. "Oh god, John." She looked up at him with a smile that forced her laughter to stay inside. "I wish we'd had more time to talk on Atlantis."

Now John just wanted to die.

* * *

"So Danny boy, how about that wager?"

Daniel sipped his coffee, and reluctantly slapped the wad of cash into General O'Neill's hand. "You know technically, I could have never won that bet. An infinite number of realities means…"

Jack smiled. "Means an infinite number of realities where you drive me insane, I get it. But the bet was that we'd actually FIND one."

The group was at the buffet table, slopping disproportioned servings of meat, pasta, and of course cake onto their plates. Off to the side Sam was busy talking with her former executive officer Lt. Colonel John Sheppard.

Teal'c stood behind Jack stoically, acting almost as his bodyguard. "Would it not be a safe assumption then to presume that the opposite is true as well?"

Jack turned and raised an eyebrow to Teal'c. "Come again T?"

Teal'c cocked his head and furrowed his brow in his typical manner. "If there are an infinite number of realities as we have seen on many occasions, would it not be safe to assume that there are just as many realities where you yourself drove Daniel Jackson to mental illness?"

"Who said anything about that being 'another' reality?" Daniel kept his tone deadpan and pulled a toothpick out of his mouth that had just recently held a piece of melon.

Jack rolled his eyes and grabbed one of the slices of the white chocolate mousse cake. He'd have to burn the calories later tonight on the elliptical, but damnit, the situation warranted some form of comfort! "Remind me again why I invited you Daniel?"

Daniel shrugged, and motioned his head over to where Sam and John were still in a deep conversation. "Ohhh something about 'I need you there Danny Boy so I don't reach across the table and kill him'?" Daniel picked up his now full plate and began to walk back to the table. "Pretty sure you mentioned coffee and cake as well…"

Jack rolled his eyes again and motioned to Teal'c. "He's crazy, I brought him to get him out of that stuffy library he calls his office. I brought 'you' to hold me back from choking the life out of that man."

Teal'c smiled, and with his plate in one hand, the other on Jack's shoulder, motioned to follow Daniel. "Do not be offended O'Neill, but after examining and comparing both of your current physical and combat prowess's, I believe it is a secure wager to assume he would sanitize the ground with you."

Jack slapped his forehead, realized it was true, and went into his deep thought mode. It wasn't often he used these portions of his brain as typically when he tried to use his higher reasoning centers, he would start uttering words like Cruvix and build a mini ZPM to run to Thor.

This whole alternate realities gig was getting to be a bit much. He'd read Landry's report on the situation with the 'Not evil but desperate' actions of another SG-1, and the dozens of teams that came through. Part of his mind was just wondering what he would have done had he been on base with so many Sam Carters, but the more logical portion of his mind that he now devoted his attention to asked a harder question.

Was the Jack O'Neill that this alternate Sheppard knew all that different? It was still him theoretically, perhaps with a few different life experiences… but it was still him… wasn't it?

Rebel Sheppard as they'd colloquially started calling him had explained what the Sam Carter of that Universe had told him. That he wasn't an evil man. But the pain of losing his family, and then realizing that the technology existed that could have saved them…

Daniel had once been put through the sarcophagus torture. It had nearly driven him insane. O'Neill had been forced to use it several times as well, but he'd always been able to fight the urge to use it more…

It was a little disturbing to think that the biggest difference between himself and that O'Neill had been a few times through the coffin of life, and it was because the Daniel there insisted on bringing it along.

What hurt the most though, was Sam. He refused to believe that he would ever do what Rebel Sheppard had said he'd done, even if it was another reality. Hell he was still trying to see if things would work out in this reality… though it wasn't going nearly as well as he wanted.

After the time travel incident to ancient Egypt… he and Sam had tried to make it work. But it wasn't long after this that they transferred her to Atlantis and again, Jack was left grasping the smoke outline of this criminally perfect woman.

She was back now, after only a year. How long would it be this time before life pulled one of them away? Jack had considered retiring, just locking himself in his cabin, fishing in the day, stargazing at night… and waiting for Carter to come by when she had the chance. After careful thought, he pushed the idea out of his mind, a week or two at the cabin on his own and he'd likely go insane.

He looked over to where Sam and John were seated, and saw them smiling and chuckling at some unheard joke. They seemed so comfortable with each other… the same unspoken bond that Jack had formed with her. It was to be expected really… she was in the same position he'd been in, and it was only natural to get close to your executive officer.

The difference was he wasn't 15 years older than her… and he had his masters in theoretical mathematics. John Sheppard understood what 'Flying Nintendo's' were... but even so…

"For cryin' out loud T…it's 'mop the floors with'… and like I said… that's why I brought you along."

Teal'c raised a single eyebrow. "Indeed."

* * *

"Wait… so technically you're not even our reality's Daniel Jackson?"

John was having fun, the old SG-1 team were certainly the story tellers he'd heard about. Even more it was nice to have intelligent conversation without competing as it often was with McKay. It reminded him of his many conversations with Elizabeth.

They'd been recounting their own encounters with Alternate realities and Daniel had just told him of one of his many years past. "Technically speaking… no. But the reality I came from is actually based and created from ours with Goa'uld technology called "The Gift of the Gods" that I'm not even going to begin to say I understand."

Jack leaned forward and snarked. "I'm still undecided as to which one is better. But then again this Danny Boy tends to have a horseshoe up his ass when it comes to dying and such so…"

Sam snorted and smiled. "Sir, you feeling okay?"

Jack furrowed his brow and looked at her with feigned offence. "Why yes, thanks for asking." His smile showed the obvious sarcasm.

Teal'c smiled and remained still as he spoke "What I believe Samantha Carter wishes to say O'Neill, is that you may have inadvertently complimented Daniel Jackson in the form of an insult."

Daniel palmed his face and muttered something in Russian before turning to Teal'c and sighing. "I think he knows that Teal'c… and he's enjoying it."

The group laughed softly at the obvious camaraderie they shared, and Jack looked to John with a deep face. "So tell me Sheppard, now that you've 'lost your alternate reality cherry'…" He noted with some slight satisfaction the way Sam resisted giggling, and Teal'c furrow his brow in confusion. "… what do you think about the whole 'infinite number of universes thing'?"

John took a sip of his coffee, and he took a deep breath. It wasn't an easy question anymore. "Well… apart from trying to get past the fact that I'm not exactly unique anymore, I think that just like infinity, it's indefinable."

Both Daniel and Sam nodded, but Jack didn't exactly like that answer. "Aw fer crying out loud, come on Sheppard. You got to see how a few different choices led to a whole different reality. Doesn't that make your head spin? Turned mine into a dreidle."

Sam smiled sweetly at Jack, he always tried to downplay how intelligent he could be. "Well sir, mathematically speaking, infinity does make people's head spin. That's why we simplify it to just something we can't understand."

John added seamlessly. "Like God." Everyone at the table turned and looked at John. He felt like he'd just committed some atrocious sin that stunned them all, like farting in an elevator. "Uh… am I missing something?"

Daniel was the only one to ask. "You believe in God?"

John nodded without hesitation. "Of course."

Daniel seemed flabbergasted. "Even after all you've seen? Ascended beings? Snakes in the head? Time travel? _Alternate Realities?"_

John shrugged nonchalantly, like he hadn't been thinking about this for almost two days straight now. "_Especially_ because of what I've seen."

Sam was silent, lost in her own thoughts. Teal'c growled slightly and leaned towards him. "Tell me then John Sheppard. What do you believe God is?"

John cocked his head as he spoke. "Nothing that we can see or hear that's for sure. God is something I think we just can't understand. Call it fate or whatever, it's just too hard for me to believe that with everything I've seen since I walked through the gate, it was created by chance alone. The math just doesn't stack up."

Teal'c growled softly again, and raised an eyebrow. "I can admire that sense of a God John Sheppard. Most unique."

Daniel seemed a bit taken aback. "What about all the different alternate realities? Is there a God for each?"

John shook his head, feeling the need to clarify himself. "No no no… like I said, it's indefinable, but if God is really omnipotent, and blah blah blah, it stands to reason for me that he could see it all and understand it all. If anything, it explains that whole 'I know what you're going to do before you do it" deal without getting rid of free will."

Daniel was amazed, never before had anyone given him this theory for how God could exist. The worst part was it made sense. "So you think God knows everything because he lets every possible thing happen? Then what's his job?"

John shrugged again. "Beats me, I'm only human. Think of it like a line segment trying to understand a cube. How the hell am I going to understand something so far beyond my physical and mental limitations? I can't, so I don't even bother trying."

Daniel and John continued to discuss the matter, with Teal'c adding in every few rounds. It was one of the most fascinating discussions John had ever had, but as they nearly finished, Jack smiled politely and nodded as if he understood what John was talking about. All he caught was that John had seen a lot through the gate, and somehow it proved God to him. He turned his head to Sam and gave his typical _'I'm lost Carter, Dumb it down for me please.'_ look.

Sam smiled, and with a sense of surprise of her own, interjected her own thoughts for the first time in the conversation. "I think you're right John… That's almost exactly what I believe." She gave a small almost awed smile and a second later looked back to Jack. "…and sir, to put it in the simplest terms, think of us as 3 dimensional, and God as 4 dimensional. We simply can't wrap our heads around it because it's impossible for us to, but it's still there."

Jack looked to John, then Sam, then John again. His voice was just mildly indignant. "Why couldn't you just say that Sheppard? Jesus, you've been hanging around Carter and McKay too much."

The group laughed again, and John became bashful. "Well sir, don't quote me on this please. I do have a reputation to keep and I'm sure McKay would spend hours ripping me on this."

Jack shook his head in disbelief.

* * *

Rodney had never been so glad to be on the Daedalus. Typically the ship was going headfirst into masses of Wraith darts and blasting away Replicators, but in this instance it was taking him home… home where he still had many things left to do.

He'd seen the videos of his alternate self, and it deeply troubled him. The alternate Sheppard had quite frankly told them of Rodney's crime, and his eagerness to turn Rodney into a human version of Swiss cheese. Rodney had vomited when they told him. The utter vile way the Alternate Rodney had succumbed to the pressure made him so sick they had to give him a glucose IV as he couldn't hold anything down.

They put him on suicide watch… John as well. It made sense as he didn't want to think about living with such knowledge.

The only reason he didn't go completely insane was that Sam had shown up to give him her support… and her solemn promise to seal the records on the incident and have everyone who knew of the alternate reality to sign non-disclosure agreements. It was standard procedure anyway, but when she had brought him the tray of Blue Jell-O in his cell, he felt slightly better.

Rodney had finally convinced himself that he'd never do that. Never ever in a billion years. But he had come to accept that he was capable of it.

He was capable of many things, he could solve mathematical equations that would make a theoretical mathematician weep in sorrow over the confusion, he could load, fire, and actually hit something with a P90.

He was capable of ruining a good relationship with Katie Brown… he was also capable of destroying 5/6ths of a solar system because he was stubborn.

He was also capable of falling in love again, and feeling that urge of obsession…. And in this reality at least, he was capable of repressing that urge, and moving forward instead of becoming fixated.

Rodney had been feeling a little different since his memory and personality resurfaced. There was a small urge of honest ambition, but not competitiveness. It was as if he wanted to do the best he could, not for the accolades, but for the people he called his family.

He'd been feeling the same for awhile now… but it was different this time. It wasn't just a growing sentiment of wanting to please his chosen family, but rather a _need_ to. As if it were the only thing that mattered.

It hurt to hear the words coming from his evil twin, and even more the words from the Alternate Sheppard about him. But now with both back to somewhat normality, the awkwardness between them was only slightly higher than usual.

"Hey! McKay!"

He turned, speak of the devil. "Sheppard… shouldn't you be on the bridge or something talking to Caldwell?"

John shook his head and sat down across from McKay in the mess hall. He had a large tray with a metal cover on top. "Nah, I'm still technically on non-active duty until we reach Atlantis and Woolsey signs off." He seemed to recede a bit, almost as if he retreated into his own skin. "He's alright you know, I only winged 'em."

McKay snorted, and sighed. "Yeah, from what Radek tells me, your evil twin was pretty pissed off that he was so battered from the crash. Something about Nanites healing him."

John shrugged and drummed his fingers along the metal cover of the tray. "Yeah, I saw that too. Can't say I'm jealous of him."

Rodney straightened. "Are you jealous of any other parts of him? Hmm?"

John instantly knew what Rodney meant, but he'd worked that out with Sam thankfully. General O'Neill had even chuckled with him about it and said he knew the feeling. "Don't tap dance Rodney… from what I've read I don't think I want to meet a Sam Carter like that."

Rodney half scoffed. "Hmm… well what about our Sam?"

This was ridiculous, John knew damn well what Rodney was getting to and the worst part was that if he'd asked him a week ago, it would have been so simple to answer.

But now? How the hell was he supposed to bury the fact that in an infinite number of realities, he'd ended up with Sam in some which way or form? The little feeling inside him that yearned for bloody massacre against the Wraith also had a little friend. And thankfully, Sam had been kind enough to not only acknowledge it, but understand it… and privately she said it was at least partially reciprocated… that was the biggest and hardest thing to swallow.

She didn't love him, hell he didn't love her either, how could they? But they liked each other, they truly enjoyed each other's company and not for frivolous reasons. John buried the edge of the feeling that had sprouted. The time for that would come later… if it ever came at all, and he'd convinced himself that it didn't matter anymore.

John understood now just how special Samantha Carter was, General O'Neill may have said it in a joking manner, but he was still serious in calling her a national treasure.

She had also had the foresight to see this potential outcome with Rodney, and thankfully had given him a weapon that she had hoped never to have to use. But John had been her undying support on Atlantis, and she owed him. "Rodney, I had a _really_ long talk with Sam about my evil twin, and you know what she said to me? She said she was okay with it. And you know what else? She told me about something that happened to her while she was still fighting the Ori…"

"What? What could she possibly have told you that can excuse the fact that you now pretty much just admitted you like her?"

John took a deep breath, when Sam had told him this he was torn between bouts of laughter, and spells of nausea. "Alright look, she swore me to secrecy and said I could tell you as long as you kept it quiet too…She got sucked into an Alternate Reality when working on some Phase Cloak thing, and as it turns out, the Alternate Sam in that reality married the Alternate 'You'"

Rodney's brows instantly shot up, his face threatened to crack the beginnings of his frown lines with a smile. "What! Really! Are you serious!" His smile instantly turned into an indignant frown. "Why didn't she ever tell me? She had plenty of chances when she was on Atlantis to tell me that!"

John resisted chuckling, and hoped the next part didn't break his friend's heart. "Calm down! Jeez… She never told you because she didn't want to tell you the next part. That Alternate Sam and McKay? They divorced, and even more, that Rodney was a billionaire dot com physicist dude." Now John couldn't help it, and cracked a smile. "Apparently when she went to go talk to him, he was convinced that being married to him had turned her… well… you know."

Rodney didn't understand. "No! No I don't know! So please do me the pleasure and courtesy of filling me in!"

John stifled his snort, and tried to keep control. When Sam had told him this in the restaurant before General O'Neill and the original SG-1 joined them, he'd been very hard pressed not to burst out laughing. "You know, he thought she… that she came to tell him she was switch hitting. "

Rodney furrowed his brow in confusion. "Say what? Use language I understand!"

"Inverted her interests? Signed a trade with another team…?"

"I don't watch sports and understand that even less! Just say it!"

John shrugged, and cracked with a snort as he said it. "Clam diving?"

Rodney was again confused, but as he thought about it for a second he suddenly came to the realization with wide eyes and his trademarked look of shock and awe. "Wha…? _You're not serious. _You're _kidding_ me. This is some cruel joke she's playing on me because she knows I won't see her again for a long time since I'm in another galaxy."

John finally fractured and began to chuckle at the thought. "I'm sorry Rodney, It was such a messed up conversation. But seriously, not a damn word to anyone about it. Sam is probably the only woman other than Teyla who could kick my ass and I'd rather not piss her off anymore than I already have. But here's my point. Define Infinity."

Rodney shook his head and with his elbows on the table muttered in sheer misery. "What? Infinity? Uhh…it's indefinable! But, unlimited, too many to count, all the individual atoms in existence don't even come close, everything after 3.14159265, and on and on. Why?"

John nodded. "That's how many realities there are. And I'm sure in at least some of them, the alternate you and her are happy." Rodney seemed a little brightened and John decided not to add the _'probably a few less than those with me and her'_ addendum. "Now do me a favor and let's stop talking about this. I already feel uncomfortable just thinking about it."

Rodney's scoff turned into a laugh. John always could make him feel better. "Yeah, uh, I guess."

"Alright. Now, there's something I'd like to say ok? And I need you to just shut up and nod your head."

"What? What are you talking about?"

"I… I know we've been a bit… well I'm trying to say I'm sorry I kinda maybe tried to choke you in the gate room back home."

Rodney winced, he recalled the incident. "Uhh… yeah…sorry for calling you a cold blooded hair gel abusing son of Kirk…among other nastier things I won't repeat."

John cringed and tugged on the back of his hair. "Look, let's put this behind us as quickly as possible okay? God knows Atlantis needs us frosty and this kind of thing is just gonna make things complicated, so..." John pulled the metal top off the tray exposing the pair of chocolate puddings underneath. "I brought a peace offering."

Rodney laughed, and reached for the spoon on his side of the tray. "Ahh yes… Chocolate heals all."

~fin


End file.
